By the looks of it, the problem stems from the players...Not the game.
KF2 skill system is far from complicated. You got a simple A or B choice each and everytime. By shooter standards, that's alright. By RPG standards, that's laughable.
What I can go behind is definitely that waaaay too many games felt the need to introduce RPG elements in their gameplay. As if you needed levelling in racing of fighting games... But I do feel that in the case of KF2, it does make some sense.
Let's be honest : Tripwire won't change something that's at the core of KF2's gameplay, five years after release. Linear leveling does work, but in a game where every perk can handle almost every situation (thanks to an ever more versatile arsenal), losing the skills would make each perk even more redundant.
And finally, I do believe that if most players don't switch for the appropriate "left or right" perk, it stems from two reasons
1) They choose an "ideal" playstyle at the start of the game and can't bother switching in the middle of the playthrough (the blame is on them)
2) Most (if not all) perks often have one option waaay more reliable or downright better than the other, making the choice a no-brainer (the blame is on Tripwire, and why everybody asks for balancing)
Anyhow, I don't think the whole system is screwing. But it does need tweaking.