I gotcha.
I wouldn't say I think that they "should" necessarily as much as that's going to happen short of introducing a bunch of random, arbitrary variables that will only serve to frustrate/piss people off.
In real life most NFL starting QB's are relatively similar from a physical skills standpoint in terms of throwing the ball. Some have stronger arms, some are more accurate, etc but ultimately they all are super talented (or they wouldn't be in the NFL at all).
In real life what differentiates guys who are good and those who aren't are things like pocket presence, the ability to accurately diagnose pre snap and post snap information, having full command of your offense (through studying/film work), and knowing situational football.
My point is that all of those things are irrelevant once a user controls a player. If I don't understand anything about football I won't be good even if I get to have Andrew Luck. I'll still be late on throws, stare down receivers, and vacate the pocket too quickly.
Conversely, if I (myself) take someone like Johnny Manziel his real life deficiencies simply won't matter because I can control all of them. I'm real good at moving in the pocket, I can get to my 3rd or 4th read in a progression, and I don't drift and always set my feet (biggest real life cause of inaccuracy FWIW).
So my point is while I would like differentiation (mostly for RB's/WR's) I don't want the game to arbitrarily make me throw the ball 20 yards away from my intended target because I happen to be using Blake Bortles, because while he'll do that IRL it's because of the stuff mentioned above. When I do everything "right" so to speak I don't want the game to punish me anyway just because.