I am sorry but I have to mock you for this. So how should one play the game according to you? Equip only weapons soldiers don’t have proficiency in? Use rage burst with pistols only? Don’t use manual aim with snipers cause it makes hem OP?
What’s the fun of playing the game without engaging the systems? If I just would want to click and watch things happen I would play AssCreed. Nice animations and no thinking required!
What you describe is not cheating it’s playing the game. One of key aspects of a game with character building, is building characters. When you Multiclass and equip your soldiers your job as a player is to find combinations that are effective. That’s a layer of gameplay.
The more open the system, the trickier it is to balance. As far as amount of skills and combinations PP isn’t that advanced - look to any RPG for comparison. And while I imagine Snapshot might have made their job trickier to due systems being simulations, rather then just numbers, it is not too much to ask for a better balanced skill system. It already got much better since release.
And again: it is not about making game strictly harder - its about improving balance in power available to players and enemies to make things fun and engaging. Better designed game will make for a better experience for everyone.