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Other than that, everyone can use anything.
Sneak synergises well with Computers, Steal and Lockpick, so it's best to use all three on the same character even if you don't tag them.
Biotech and Electronics are pretty independent so anyone can do them.
There are 0 (zero) mandatory fights, and there are even achievements for finishing the game without entering combat.
Some endings are locked behind combat, but for both fights you have a ton of potential leverage with Sneak or Speech so it's not very difficult.
What is better: persuasion, streewise or impersonation?
Skill Monkey gives a bonus to Science Skills AND Stealth skills, thus you probably don't want to split the science and stealth skills to multiple characters, because you don't want to use Skill Monkey on TWO Characters, if you can get away with only having it on one.
The most obvious solution is, to give Skill Monkey to Faythe and let her handle all the Skillchecks. Since she also can get "Thief" as a personal feat (depending on how you answer her little psycholgical crisis after her recruitment mission is done, she either gets "Thief" or "Assassin"), "Thief" earns 25% extra learning points / lp in all Stealth skills (= Lockpick, Steal, Sneak), so Faythe really is predestined to being the Skill Monkey.
The only obvious alternative is, if you are playing a Mastermind Mainchar, then you have enough tags to do everything on your MainChar, and enough feats that you don't care wether you also give him Skill Monkey.
To really optimize your run, you need quite some Meta-knowledge: either you played the game before, or you look things up on the Wiki, or ask questions in the forum (- which you did).
Examples:
Thief Faythe does not need a Steal tag, you can skip that one.
Thief Faythe technically does not need a Sneak tag (- if you do every sneak situation there is perfectly, and give her every Token with Sneaking lp, she can get to Sneak 9 without a tag.) But giving her a Sneak Tag makes things a lot easier, and she can get away with one Stealth Feat less (or vice versa).
As for Biotech: I used to prefer it tagged, but there is exactly one case, where you don't need it tagged: if your MainChar has Healing Factor as starting feat : then he gets 100% extra Biotech lp. (Or of course if you don't care about the very few Biotech 9 skillchecks at all; and you are not bothered by a bit of back and forth and not getting your implants and chips at the very earliest occasions - you will get to Biotech 8 eventually even without tag).
(P.S.: even if your MainChar handles Biotech, it is still advised to pay the trainer to have Faythe learn a bit of Biotech, so she can do everything in the Crypt / during the "Eye heist".)
Since Faythe is short on tags, it sometimes comes down to wether you prefer her to have a weapons tag, which is very helpful in keeping her combat relevant, or have the sneak tag (which is optional, if she has "Thief" and "Skill Monkey" and three of the Sneak feats and does partake in 95% of all possible sneak occasions / maximize sneak lp).
Long story short: look at the "Player submitted builds" thread. Or let me present you my two versions of Skill Monkey Faythe. Or even better: the tl;dr synthesis at the end.
Screenshots:
If you always take Electronics over Computers, and Computers over Lockpick, and give Faythe all the Tokens (especially the Science Tokens), you will end up with something like this. (Note: don't use the Steal tag: use it as a Weapons tag, or Sneak if you want easy sneaking; or CS if you have touble getting her Takedown to 95 (= her CS to 5).
https://steamcommunity.com/sharedfiles/filedetails/?id=3080878089
If you do your "Healing Factor" MainChar run, you can get away with something like this (- note: I changed Token usage - two "Field surgeon" for my MC and two "Breach Team" for Faythe meant significantly less Computers skill, as she did not get all her usual Science tokens).
https://steamcommunity.com/sharedfiles/filedetails/?id=3151968156
On this playthrough I went with more Combat (see Combat Rating 80) and less Sneaking (see Stealth Rating 41 vs 49 before), thus Sneak didn't end up at Level 11... (as you might have assumed looking at the first Screenshot). Level 10 Sneak is mighty fine.
Edit: damnit - too many edits. I deleted my tl;dr - let's redo it:
tl;dr
If your MainChar is NOT Healing Factor or Mastermind, this is how Faythe should look like:
Tags: Thief Faythe tags Biotech, Computers, Electronics, Lockpick, Weapon. Wether you do Weapon tag last or Electronics tag last, depends on wether you want less frustrating fights (= Electronics last) or less back and forth / hassle with very close Electronics checks. (see last spoiler block). (Alternatively use a Sneak tag instead of the Weapons tag) Edit: or a Sneak tag instead of the Biotech tag (- see followup comment)
Feats: Thief Faythe takes Ghost, Throat Slitter, Main Weapons Feat, Tunnel Runner (or maybe Prowler instead for the Eye heist, if you don't have that Sneak tag), Skill Monkey, Master Blaster, Bonus (if Faythe reaches Level 8 by either going Cult Leader or doing the first part of the game with 3 until you can recruit Harbinger / Knurl).
Implant(s): Faythe always gets the very first Dex implant, as she needs that 1 extra AP in assassinating Mercy perfectly with all Takedowns (- if you are plannig on doing that). - Alternatives would involve 2nd Wind or Tunnel Runner early instead of the weapons feat. (See also "3rd" in the Spoiler)
If you really want an additional implant e.g. Eye for better Acc and Glare (Thermal) Chip etc. or Spine/Str for Armored Warfare feat, you can still take Bionic before the end - or instead of Tunnel Runner. (Well; wether you want Tunnel Runner (or maybe need Prowler instead) for the Eye heist, depends on wether you have a Sneak tag, and maybe a bit on how good you are / how long you have worked on it / wether you watched a Step by Step video etc.)
Three more complicated optimizations:
1st: If you don't have a lot of Energy Cell users (and already have a Energy Weapon of the right kind by that time), it is viable to start with Master Blaster instead of the Main Weapons skill.
2nd: It is also viable to push Skill Monkey one slot back, but only advisable if you don't happen to make it to Lockpick 10 (or Computers 10, which I think is actually impossible that early) for looting the Lander Level (Mission Control Level 7) before you go Zone Yellow and Red. You need to have done Zone Yellow and Red I think, before you reach Computers 10, thus you can "afford" to push Skill Monkey one slot back in favor of more accuracy which you might want to have for Yellow and Red (= Weapons feat or Master Blaster); Differingly in my Healing Factor playthrough Faythe reached Lockpick 10 early (before Zone Yellow and Red) by using the Breach Team tokens (and doing a little Lockpicking instead of Computers here and there), therefore early Skill Monkey was useful and needed, as it allowed me to get to LockPick10 and loot the Lander Level before even going Zone Yellow / Red; so it depends, wether you want to do Yellow / Red with overall better equipment, or better accuracy on Faythe, wether you should pick Skill Monkey before her 2nd Weapons feat or vice versa.
3rd is somewhat historical: in Early Access I used to take 2nd WInd instead of Tunnel Runner, because back then Tunnelrunner was a worse version; and back then I might have taken that even before taking the first Weapons feat, as I needed it for all perfect Black Hand Fortress takedowns, and she didn't have that next level-up yet? Don't quite remember. The importance of all perfect takedowns was only ever in my mind anyway, and with my last playthrough, I even did the Frontal Assault II at Black Hand and did not do the sneaking at all... - and even with the first+second playthrough after release, I just decided that having the Master Blaster (=first wepaons feat) early is more important than taking down those (otherwise) two impossible guys...
Electronics Tag can be done last, without missing out on anything: After the Shuttle Bay go directly to the Church Archivar in the Church Habitat: he tells you about the Machine. Then you choose your favorite Habitat Faction, earn a meeting with the Leader, promise him the Machine; get sent to the Mainentance Deck / ECLSS, where you meet Eli, who can overclock implants for 2000 credits each: Faythe's Int implant is always the first to get done, as she needs Electronics 6 on multiple occasions in the Habitat, which by this time you can only reach with the tag; don't forget to revisit the Electronics 6 check in Mission Control you could not do before, after returning from the Habitat (one of the rooms has a Subdermal Implant and 12 Energy Cells and a EMPulse and a Brainwave Disruptor grenade iirc.)
Edit: Sorry, the post kept getting longer and longer, as too much (especially concerning perfect sneak runs) depends on what tags and feats Faythe actually has when attempting certain sneak runs / scenarios. - If you compare my tl;dr synthesis with my actual screenshots, you can see that there might be a little "fat" here and there I have cut, just by deciding not to go for the perfect solution here and there; or maybe on the contrary: by always going for the perfect solution skilled up sneak enough to be able to cut a tag or a feat. - Oftentimes what counts as "optimal" is in the eye of the beholder anyway. - E.g. if you are unsure wether you can do the Eye heist, it's best to keep a feat open and do a save: maybe you don't need a 3rd Sneak feat at all, because your sneak is high enough (e.g. tagged), or you do better with Prowler, or better with Tunnelrunner. Technically speaking one does not have to make it out undetected: getting in and stealing the eye, and then setting off the Alarm still lets you keep the eye... (- as you run out while the Alarm is going off, and don't actually get caught; edit: but of course you naturally want to do it perfect without detection: earning extra sneak lp as reward).
The important thing is, that Faythe saves the tag and thus can afford to tag both Sneak and Weapon (- in addiion to Computers and Electronics and Lockpick.)
In the grand scheme of things it is relatively unimportant wether MainChar just uses a tag or does a Healing Factor playthrough, or we even let Jed have the Biotech tag.
Maybe it's time for me to do a Cult Leader run without Evans, but with Jed and Faythe and Harbinger. - I'd like to see Harbinger reach level 10, Faythe 8 again, and this time MainChar also 8 ( I didn't use Educated last time). Jed most likely will not reach level 9, but that's ok.
Having nobody with a real good Initiative probably means a pretty lame playthrough, but if I'm doing it, I'm doing it for the Photo-Finish as my 4th playthrough since release, and just to work a bit more on some of my missing achievements: might give Mercy a chance and finally play a Church run.
Edit: As for the pacifist run? I haven't done it yet, because I already know too much ;-)
(I will do it some time for the three Pacifist Achievements.)
As far as I know, it has two main plot twists, and despite what you might be expecting, you are not exactly the one engineering them. It's simply not the way the story is written. - It's more like you are living through changing tides of history and come out alive and aligned with the "correct" / overall best situation for the ship (and the future colony), but not exactly due to your machinations, but more due to following "stronger arguments" twice. - By not choosing to fight, you avoid death, but you are not exactly the master of history. The game teaches a very stoic approach: try not to care too much about things you can not change. You might find this to be anticlimactic, or a good lesson in stoic philosophy - depending on wether you expected to be the great Hero, as in most other games, or not.- I probably already said too much. You will see. - Or you can add 2+2, depending on how much you have already read on the forums about the 7 possible endings, and the diferent ways you end up in them,
Overall the endings reminded me a bit of "The Life and Suffering of Sir Brante": you have your role to play, before it is all over; you live through tumultuous times: nothing will be the same. When you manage to come out unharmed, with your friends alive, and with still a bit of societal standing in the new order of things, that's all you can ever hope for; but nothing will ever be the same again. The Earth shifts under your feet. If you can remain standing, that's already a win.
Pretty much every other attempt to imprint your own handwriting onto history, leads to bleaker and bleaker outcomes, furiously tumbling forward even more brutally or chaotically. The best you can hope for is carve out a tiny piece of freedom and peace for yourself. Every attempt to accomplish more for the whole of society only leads into deeper trouble.
Another topic: I'm about to enter the Factory when the game notified me to go back and do the Courthouse kill quests. However as I've build my character to be as combat-free as possible (and I'm not very good at managing the 3 companions yet , namely Faythe, Jed and Evans) I'm struggling a lot.
What advice could you give to me WITHOUT starting the whole game over to be have a more balanced approach?
This really depends on what your companions look like. With a party of 4 you should be able to easily beat every fight in the game regardless of how your main character is built.
Would you like to share screenshots of your companions' character sheets and inventories? It's so we can give specific advice that'd be most useful.
It definitely is frustrating to feel like you can't shoot at anything. I'd need to see what your party looks like to give specific advice, but until then you can check out the official youtube tutorials for combat:
https://www.youtube.com/watch?v=0x7XkqwAgvA&t=180s&pp=ygURaXJvbiB0b3dlciBzdHVkaW8%3D
https://www.youtube.com/watch?v=Q_SA5ErDq0A&pp=ygURaXJvbiB0b3dlciBzdHVkaW8%3D
I purchased the game with this mindset, but these mandatory Courthouse shoot-outs are just annoying.
Thank you for the tips, I'll have a look at them later.
They're not mandatory, the reminder when you leave for the Factory is just so you know that they won't be available later in case you forgot about them.
There's nothing mandatory about doing them and if you don't plan on fighting, they bring no benefits.