At no point in madden 16 do I believe I ever used the left stick to put my guy in a "better" position to get a catch. Nor did I ever see any youtube videos or forum posts about using the left stick to achieve better animation or catch results. Now if I was just under a rock, and this was something that was commonly done, then I understand that view point. The use of "advanced" supplemental mechanics supplemental mechanics, no matter how small, is still user skill. I'd maintain that merely hitting a button is not.
I disagree with your analogy. I don't want to grab a football and go outside, because I want to play NFL football which I can't do through any other medium. I never actually played NFL head coach, but to my knowledge, in that game you'd build the team, call the plays and actually see the play in the actual game like it were madden, you just wouldn't control anything. Is that your ideal game? That's a situation where the user "game" skill is completely removed and replaced solely with strategy and letting the ratings play out in their truest form. I imagine that for most that wasn't what they were looking for. For people to play a game like madden user skill inherently just has to play a role. For example it appears the right stick ball carrier moves will take some skill to best utilize. That's stick skill dictating gameplay. When a person users a D lineman and perfectly times something and uses the stick to take a better angle, that's stick skill dictating gameplay. When a qb in the pocket uses the avoidance step up feature and breaks a sack because of it, that's stick skill dictating gameplay. When a user safety, even with no switch rules enabled, breaks down and picks off a pass, that's stick skills dictating gameplay.
Now don't get me wrong, I believe I understand your argument that there's a balance that you want to strike, and that balance is going to vary from person to person. But to me a user qb being able to override all the traits and awareness a qb has and allowing him to play infinitely above his rating (I acknowledge this isn't an allowance but simply has to exist for the game to be played), users being able to play above their defensive linemans ability via user control, etc...to have these things present that take user play into consideration but then be so stringent on switching to a wr and hitting a button (if that's the only action involved, which I believe it is) seems unnecessary. I won't address the tackle switching point, although I wouldn't be thrilled playing with such a rule I do see why some people, like yourself, find it necessary and enjoyable to play with.