So, just going to list bits and pieces of my personal theory after finishing this 100% *SPOILERS*

[AestheticGamer aka Dusk Golem]

-So I never pulled this much from the original game, but in this reimagining I am pretty sure there are strong themes here of gender identity. I know many people have joked about this theory before, but I think there's actual evidence here. The only bathrooms Madotsuki ever enters in YYDD are men's restrooms. To get the secret ending (and to finish the game) you have to activate the symbol of Venus aka the symbol representing female, and then enter into a giant Venus symbol to enter. In the sketchbook there's two pictures you get of Madotsuki that are practically the same, but one with her eyes closed and one with them open. Most related pictures are next to each other in her Dream Diary, but for this one a picture of her eyes closed are next to KyuuKyuu-kun, and her picture of her eyes open is a few pages later next to the picture of the feminine mannequin. Literally eyes closed next to the most phallic character in the game, eyes opened next to the character most with a 'female form'. Add to this the area you get the flute in the mall looks even more like a clinic than the original, and to add to this O-Man's updated look looks a lot more like a doctor, there's character's alluding to genitalia-esque objects on the walls, and E-Man who you go to see in the clinic gives you the Flute. I don't know quite yet on this one if I'm reaching here, but all I'll say is I never got this theory in the original but have it pretty strongly in YNDD.

-I'm going to cover this more in the following points, but I think Madotsuki is a shut-off NEET not because she was♥♥♥♥♥♥♥(I don't think there's evidence for that) or even because of gender identity things. I think it's more straight forward, she experienced multiple scars over the years that made her more reclusive and eventually just shut off from the world. Rather than one traumatic event she experienced several over-time events that made her close off. This also ties in well to unlocking the final door by re-experiencing everything and then when you go out of your apartment having to survive your inner fears (that shadow thing) to get the happy ending.

-Monoko is dead. In the original game the stop/start light changing her form was a bit suspicious and the specifics of the differences, but this remake somewhat spells it out where you can reach her by going to the world end event related to death to find her, and when we see her more twisted form she gets surrounded by blue flames (if you don't know, in Japan blue flames are associated with death and spirits). Also would explain why her form in the remake is so underplayed to Monoe and hidden away. This one I don't think many would disagree with as it's kind of blatant. Monoko's area achievement is also titled, "Doomed", and the description for this is that you played with a 'lonely child'.

-I know many people theorize that Monoko and Monoe are sisters (and for obvious reasons to suspect this), but I don't think Monoe is crying over a dead sister from the evidence. I'm more inclined to believe the black and white similarities have more to do with 'ex-friends', they're just memories to Madotsuki now. Monoko died at some point, probably when Madotsuki was young. If you look at the recently released Yume Nikki character height comparision chart, Monoko is considerably shorter than either Madotsuki or Monoe. I think she died while Madotsuki was of a similar age. I also am wondering if hide and seek had something to do with her death? In the original game she's hiding in the middle of nowhere, and in the remake she plays hide and seek with you until you find her in her twisted blue-flame form. I'm wondering if she died playing some children's game like hide'n'seek?

-Monoe experienced something traumatic and Madostuki failed to help her. The picture you collect fragments for are of someone following Monoe, it's not a voluntary picture. Monoe will not let you get close to her, implying that she both doesn't want to be touched and wants Madotsuki to stay away. Eventually when you keep following her you get to the place with a wall made of a giant zipper (like you see on the front of pants) which keeps bulging and un-bulging. You unzip the zipper and inside you find KyuuKyuu-kun rubbing the pole vigorously right next to Monoe, who is crying. When you approach her, Madotsuki begins crying too. To the right of the Lantern event you can find Madotsuki in a drawer crying (and you get a picture of Madotsuki's umbrella power when you do this, which notably is how you begin to get Monoe running away from you... Madotsuki's tears). If you come back to the KyuuKyuu-kun location after beating the area, you get the FACE event, which is well documented in how sexual it is combined with being next to KyuuKyuu-kun. I'm not going to cement saying I believe she was♥♥♥♥♥♥♥ but I think it's hard to doubt there's something sexual going on here with Monoe but she seemed upset at Madotsuki for getting in her business, and Madotsuki seems to not forgive herself for not being able to help her. I think they no longer are friends but once were, which is why Madotsuki seems to care about her and why Monoe has a violent reaction to Madotsuki. I also will add the achievement for hitting this story of Madotsuki and Monoe crying with Kyuukuu-kun rubbing above Monoe is titled "Deep Dream", with the description, "Too young for this".

-Poniko is the other friend of Madotsuki. I know many think with the balloon things that it signifies Poniko was♥♥♥♥♥♥♥or something, but I think the idea is more those are lost balloons that have drifted to Poniko. Madotsuki was drifting (like she literally does in the level) through her life and ultimately floats over to Poniko. Poniko isn't greyed out like the others since she's a current 'friend', also implying this is later than several of the other events (which also may explain why Madotsuki was 'drifting' while trying to deal with her past). But Poniko doesn't actually seem to like Madostuki that much, we see her in her room drawing (which implies we've been to her room sometime in the past). When you approach her she covers up what she's doing like she doesn't want you to see (but there is a drawing on the wall). The only thing you can really do with her is annoy her, represented here by turning the lights on and off. When you do that enough and bother her enough Poniko 'screams' and turns into Uboa. I think Madotsuki IS friends with Poniko, but Poniko finds Madotsuki super annoying and Madotsuki is afraid of annoying/upsetting her and has seen her scary side behind closed doors. The achievement for this area is also "False Appearances", but to mention it's also noteworthy details of her room changes in light and dark which might also hint at Poniko being two-faced.

-Now I don't think Madotsuki is a literal murderer. In the original game ♥♥♥♥♥♥-san gives you the stoplight effect (also tying that in the original to death), which lets you stop other people and shows Monoko as dead. I think ♥♥♥♥♥♥-san is the 'trigger' that lets off everything Madotsuki had stored away to explode into full-blown depression and fear. ♥♥♥♥♥♥-san evidently died in a traffic accident, and it seems Madostuki views that she killed him. Maybe he was depressed or she could've done something to stop him or change things, but I think she holds herself as responsible for not being able to save him. I will admit something though, I do not have any idea why Onsen-san is connected to ♥♥♥♥♥♥-san. Frankly while I guess traffic accident and I'm pretty sure I'm right about Madotsuki's feelings and place here, the exact details of Shintai-san and Onsen-san I feel have more to be read into. When you finish this area, you get an achievement titled, "Remorse", which has the description, "Why did you do it?". Maybe Madotsuki pushed this man to a point he died (maybe either via something foolish and an accident or suicide), and Madotsuki greatly regrets it?

UPDATE: So I thought about it more, and Onsen-san represents a hot spring or bathtub. Could it be that Madotsuki was cutting herself or attempted suicide in a bathtub? You cut up Onsen-san and then see Shintai-san dead in the road. Maybe you were rescued or rushed but somebody died in an accident saving you after cutting yourself? This is more of a stretch than the other things I admit, but might Madotsuki cutting Onsen-san represent herself cutting herself in the bath? You also notably NEVER see Madotsuki's wrists because she wears that long sweater all the time, even in her own house. This is more of a stretch than the rest of my theory, but I got thinking about it. Onsen-san also turns blue in the original game when you cut it rather than disappearing, a color associated with a corpse dying (but notable Onsen-san in the original doesn't die, just stops moving and turns blue).

-This one is really obvious since the original, but Madotsuki has some interest in ancient culture and the occult. It's littered over both games, but one of the 'big events' in this game is Madotsuki seeing the UFO with people over the city, and next to that is the pure white flower field. In the original game this leads to the area Madotsuki gets the ghost power by chasing the singular ghost, but white flowers do mean purity among other things. I think Madotsuki may have been embarrassed by her love of these things, viewing it as geeky or something she has to hide away from others to protect herself but is precious to her. Her interest of the occult may also have sprung from her early life exposure to death, which might be another meaning of the field of flowers linking to the ghost power in the original.

-The mall event with the mannequins new to this remake I'm pretty sure is related to my original point, Madotsuki's desire to live up to the image of being a woman. The mannequins are intimidating to her and notably all of them strike feminine poses. They can't get Madotsuki when she's in the light but can when she's in darkness, and the area ends when she passes by several mannequins on pedestals and then gets into her bed with all of these mannequins suddenly surrounding her. I take this as Madotsuki's fear of being judged, I think she wants to appease to the image of a woman but is also intimidated by it. I don't think this is uncommon for those overcoming walls for their own gender identity or even simply body image, and just even the general fear of people talking behind your back or being two-faced with you. I think this area represents that part for why she closes off from the judgement (or perceived judgement) of others. When you complete this area you also get the achievement, "Distrust".

-This one is the most obvious, but the beginning is her contemplating suicide. The thought of going outside again makes her want to kill herself. The game has her tackling the big areas in her life that's made her a shut-in, and ultimately overcoming her own fear to go outside again.

-The secret ending with Seccom Masada-sensei deliberately says in the achievements that she stays in her dream as it's cozy. It does point that there was a figure in Madotsuki's life she found comfort in. Going by the original game and YNDD, something happened where they parted ways. In the original the spaceship crashes, and in the remake her being tempted to stay in this place because he's here would imply she can't just go see him anymore. I am thinking that Seccom Masada-sensei probably moved away, represented in her dream as him on a spaceship going to Mars. Their relationship didn't end badly like many others, just he's too far away to reach now.

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Of course, this is all just my own theories, but what do y'all think?

[Deep Weeb]

To me, Poniko/Uboa represents Madotsuki's mother, it's shown both in the official artwork and in the game that Poniko is the tallest of the human characters (and based on that alone I would assume she's also the oldest)
But in the Pink Sea, you can see some sperm-like creaturas above Poniko's (castle?). Nitro Rad believes that the Cone-shaped structures represent a womb, but personally I believe that the cones actually represent some sort of contraceptive method, as you can see since all the "sperms" are kept outside her cozy and safe womb-like room.
Madotsuki can't leave once she enters into the room (although this most likely due the linear nature of this remake). This would represent that Madotsuki was result of an unintended pregnancy. This can be told by Poniko's disgust towards you. She didn't wanted a child bothering her. Her "safe space" has been invaded by you
And after Madotsuki flickers the lights, when everything goes dark (how Uboa appears on this game is pretty lame, you can't even see it for more that 1 second and as a lame jumpscare, but the sound playing when the lights go out is pretty interesting) you can hear a very heavy, furious breathing. Clearly coming for Poniko. She's really annoyed by your presence and wants you gone. The sound hear when Madotsuki walk towards Poniko sound like as if something broke, meaning that Madotsuki has a very abusive mother.

I didn't read to much into the "False Appaerances" achievement, other than canonizing that Poniko and Uboa are a same entity. Maybe it's could represent how everybody see her as a sweet-loving mother on the outside while in reality she's abusive and aggresive towards her child, and nobody seems to be aware of this? (This actually happens a lot in real life)

[Merle is a dog]

Some more interesting theories. I love how people are already coming up with things. A lot of these all make sense too.

[RokuroCarisu]

Originally posted by Deep Weeb:

To me, Poniko/Uboa represents Madotsuki's mother, it's shown both in the official artwork and in the game that Poniko is the tallest of the human characters (and based on that alone I would assume she's also the oldest)
But in the Pink Sea, you can see some sperm-like creaturas above Poniko's (castle?). Nitro Rad believes that the Cone-shaped structures represent a womb, but personally I believe that the cones actually represent some sort of contraceptive method, as you can see since all the "sperms" are kept outside her cozy and safe womb-like room.

Nitro Rad doesn't believe that, he came up with that speculation on the spot because he didn't realize what those "sperms" are actually meant to be: Nopperabou Ghosts, like the one that gives you the Nopperabou effect in the original game. Poniko's house is no womb, it's haunted.

As far as I'm concerned, Uboa and everything else in Poniko's room represents nyctophobia, the fear of the dark, and specifically the way how perfectly normal things can start looking spooky as soon as the lights go out. Pretty much every child is familiar with that.

For the game as whole: I think it's about Madotsuki facing a mix of familiar imagery from the real world and more or less abstract representations of all her fears that keep her from leaving her room in her dreams.