You'll find lots of ways to upgrade both playable characters, and it's worth thinking carefully about your choices since you can't max everything in one go. Each character gets their own skill trees that work with supplements you collect, plus training manuals that unlock new branches when you find them in the world.

Playing around with stealth upgrades is pretty interesting, especially stuff like crafting silencers and improving your listen mode to spot enemies better. If you're more into aggressive play, there's some really good options in the close quarters tree that'll help you craft better melee weapons and get more momentum in fights. The ordnance skills let you make stronger pipe bombs, and the firearms tree has nice improvements for your weapons.

Some really useful upgrades to look out for: crafting silencers is huge for stealth players, explosive arrows add some nice variety to combat, and the listen mode clarity helps spot enemies through walls better. Getting the ability to craft more items from the same resources is definitely worth it too. Just remember, you'll need to start a new game+ if you want to fully upgrade everything, since there aren't enough supplements in one playthrough to max out all the skills. Maybe interesting - try focusing on upgrades that match your playstyle first, since you won't be able to get everything right away.