What, no two-minute drill complaints?
I agree that the penalties are out of whack. Way too many facemasks, probably too few holdings and pass interference.
Running game AI is really odd. Way too many backs freelancing running backwards & sideways - football is a north-south game once you're past the line of scrimmage.
I actually don't mind the emotional reactions & defining moments. They're not my favorite feature, but I'll live.
IMO, franchises starting with a custom playbook shouldn't be penalized so heavily - alternately, make it an optional penalty. If I want the Packers to run a Tampa 2 scheme or go all Raiders-deep-pass, that's my choice as a gamer, not as a football historian. I'd love to run a heavy I form or 3TE 1WR sets... Just set an initial custom playbook at "learned" and be done with it.
Speaking of playbooks, the play editor needs a lot of work. Being able to actually make a running play would be a plus. Being able to organize your playbook in a sensible fashion, even after adding plays from the other guys, would be a plus. Being able to use numbers in play naming would be trivially awesome.
Being able to flip custom plays would be tremendously helpful. Likewise being able to adjust such plays on the fly. Why I can't set my man cover plays to press, I have no idea.
Coach hiring needs work. Nobody comes poaching my OVR 99 coordinators as head coach candidates, or my skilled position coaches as potential coordinators. Hiring of coaches should be delayed until after the Super Bowl every year; firing can happen whenever.
The draft & scouting, as it is, are "very rewarding".
It's fun - not very realistic, but very fun. On a meta-level,
some teams are better than others at scouting overall, but that's not necessarily reflected as well as it might be in the GM ratings. For example, Ted Tedson of the Packers really isn't that good of a scout in the game, when in reality the franchise has a pretty fabulous track record of finding unknown players like Aaron Kampman (4th round!), Nick Barnett (1st round, but "Nick who?"), Greg Jennings & Nick Collins (both 2nd rounders "from nowhere"). I don't know how easy it is to reflect that in the game (scout hiring doesn't sound like fun).
At the same time, if you actually coach games & call plays, having a fabulous roster isn't enough - you have to be a good play-caller to win.