There are a lot of perks in skill tree which I actually just don't know how to use.
Most of the other perks are +N damage to N weapon, +N to crit chance with N weapon, +N to HP restoration speed and such, which have no use at all since all of these "plus N" can be acquired with guns and armor stats.
The only category I've found useful in some sort is Intelligence, which has some influence on the fight and stealth by decreasing the time you can hack the camera etc.
In general, I found character's upgrade system very confusing. In most cases, I just don't know how to spend my skill points..
Throwing Knives perk (Cool) makes me lost my knives without any chance to return it, as far as I can see. So you can throw the legendary knife and loose it forever.
Hidden Dragon perk (Cool), I just don't know how to execute. Description says that it allows to jump on enemy from above and kill him, crushing his skull by ground. Is it even possible? What key should I use? I've never succeed to perform this trick.
Commando perk (Cool) - you cannot be detected under water. I've completed about 80% of the game by now and never had a fight near the deep water where I need to hide from enemies.
A lot of perks in Cool category related to poison. Increasing poison duration, knives are now poisoned, deal more damage with poison, doubled damage with poison. What is poison? How do actually apply this "poison" (whatever it is) on enemy? No way I can poison somebody with knives only?
Human Shield perk (Body) - I don't know how to use it as well. It says that this perks decreasing incoming damage when you grabbing the enemy. But I can only grab the enemy from behind, which is impossible to do during the combat. And in stealth mode, there is obviously no incoming damage to decrease.
The Rock (Body) - enemies cannot knock you down. The only time when enemy knocked be down happened during the fight with Animals boss, and it was scripted event so I did not even loose HP. Or what does "knocking down" mean?
Stronger Together (Body) - increases the amount of damage you do while carrying a body. But I can't use the gun or other weapon while carrying a body.
Most of the other perks are +N damage to N weapon, +N to crit chance with N weapon, +N to HP restoration speed and such, which have no use at all since all of these "plus N" can be acquired with guns and armor stats.
The only category I've found useful in some sort is Intelligence, which has some influence on the fight and stealth by decreasing the time you can hack the camera etc.
In general, I found character's upgrade system very confusing. In most cases, I just don't know how to spend my skill points..