Have I somehow missed half of the game?

[Roderick]

Just done with the story... but there are so many achievements I have no clue of... Oo
Why so many spaces for different staffs? I have found like three?
There are also bosses I couldn't beat yet... a dragon protecting an mystic item f.e. But why? Is that item needed for something? Is there more of the game in a higher difficulty?
There are soldiers north of the popes palace which I wasn't allowed to fight all the time, so I was sure there is more, but after finishing the story I just get kicked to the main menu. What's up there? Why can't I fight those soldiers? And I never met that guy again who wanted the ships crew list. Never entered the lower deck becaue I never got a key.

I am highly confused.

[Valmond]

There are a ton of things in the game. The soldiers cannot be fought. However. There are time based events that adds onto the story. Such as how Ethan ends up on a certain continent in Witch Spring 4.

The diary for Livya. A side event in the mines, etc.

To get the key to the ship. You have to get the list from the captain's quarter, and give it to Ethan in Lalaque cell.

[Fredo]

there is a lot of thing the dev put in the game without telling you anywhere how to achieve it, easter egg of sort, majority of weapon space are for melee weapons, the one the dragon guarding was one of them.
I don't know how to formart spoiler so I will just make a list of clues here if you interested in platinum the game.
Depend on how much you completed the game, the ending cutscene will adjust itself to add/remove section of relevant characters.

======= SPOILER WARNING ======
- [Missable] Jade's table after Ethan event (pre Elyshion Shrine)
- [Missable] Shipwreck diary - Livya (pre Elyshion Shrine)
- [Missable] Check every walkable passage near Matt's prison cell.
- [Missable - Lore and achievement] Kate & Livya - Go back to Reina before continue.

- Acient lightning dragon - Reina (chapter 7) - Evolvable
- Aimhard spring area - Soul Incinerator - No shield
- Lalaque Forest Nothwest - Elks - Aimhard blessing
- Luna's house (you said you found 3 staves so this one is prob finished).
- Red Beard - 4 times
- Red Beard - Frozen key - an ice door somewhere on snow mountain
- Eison (outside your house) - Aged Lalaque Berry
- Eison - East side of Witch forest - 3 events
- Eison - North East of South Island - Rabbit
- Eison - Pudding cave
- Ludina's altar - Frozen Hilt - timed
- Boar Plain > West Elysion Shrine path > Dragon valley > City - Zirconia Dragon Egg - Pet equip 'Tia'.
- Nag Kanna for second bot
- Blast (Final Lava area Elite) - Frozen Heart
- Fox cave - Pink orb accessory
- Giant dragon after Elysion Shrine.

- [Minor - Achievement] Enchant any weapon to above 50% (lalaque blacksmith)
- [Minor - Achievement] Weapon shop in the city.
- [Minor] The forge in Matt's house (Kanna's house).
- [Minor - Item] The lone guard east side of city.
- [Minor - Lore only] The guard in Death's Squad prison (chapter 7) - The forest outside
- [Minor] The table of the big guard in tavern after his friend has left
- [Minor - Dialog only] Table in Anna's house - After Aimhard shrine (before & after Elyshion shrine).