Here is a list of other things just from the top of my head:
1. Most plays (offensive and defensive) have been rendered useless somewhere along the way with some game engine change.
2. Spamming WR2 slants (with the right QB and WR2) is often a lethal offense, and there is very little to nothing the defense can do to slow it down.
3. QB's severely overuse TE's and RB checkdowns, and it can be very difficult to get them to throw to WR's.
4. Blowouts used to be a real thing. Somewhere along the way, some sort of "anti-blowout" or "parity-forcing" code was introduced. If you get too far ahead too quickly in a game, the sim completely and entirely nerfs your entire team for the rest of the game. This then leads to a tough game, and occasionally a loss, to an AI team that doesn't even belong on the same field. Just let the blowouts happen.
5. The secondary is WAY too fast in recognizing the ball was thrown and changing direction. I can't tell you how many times I've seen a CB covering a go route come back and knock down a dump off to the RB at the line of scrimmage. Complete nonsense.
6. Somewhat conversely, the defender covering a RB in the flat often simply runs straight past him into the backfield giving the offense an easy huge gain on the dump off when the RB gets behind him.
7. Games where a team completely and utterly dominates statistically and then loses happen at an insanely high rate. I think this is related to the "anti-blowout" or "parity-forcing" code mentioned earlier.
I'm sure there are so many more things I could come up with, but these are some of the biggest I can think of right now.