I don't have the game, but it sounds like it's similar to last year's "tale of two halves", where the game actually makes it happen instead of it just being my players "getting lucky" on their rolls on the first half and then it coming back to normal in the second, and vice versa.
I have seen the CPU play completely different (again, in M12) and I check ratings and it's not as though I was holding down a top team and they broke out. Likewise when it works in my team's favor. I check ratings and the other team didn't suck (or I know my QB isn't that good, yet he looks like Montana and I don't play any different - the players are just suddenly being perfect).
I agree that things like that SOMETIMES happen in real life, and it would be nice if it was more than just randomness (and if it's tied to skill level, i.e. on All-Madden but not All-Pro, well that's already overly artificial since it only occurs on one setting) - like a trait where players are fine as long as things go their way, but if the other team does mount a rally, they panic, especially on the road. They get too aggressive, exposing themselves to more mistakes, etc. Then it would be more realistic. I feel that skills don't change - but stamina and decision-making (especially) does and maybe should go hand-in-hand (player feels like he's losing a step so he may over-commit to compensate, etc).
If I have a well-coached, highly-skilled and disciplined (good AWR and such) defense, why would they ever fall apart if my playcalling stays on point? If they do get broken down and come back on, it shouldn't be because it's a "tale of two halves" game. It should be because the other offense continued to work, my offense doesn't do what they need to do to get 1st downs (maybe I got TOO conservative like Redskins did with RG3) or commits turnovers, and even then, it shouldn't always happen (like it didn't with the Redskins - they still won because Brees failed the comeback).
I agree that sometimes people might not be handling the situation right. I know there's been times where I didn't in M12. I either got too aggressive in my playcalling, taking guys out of position and not just letting them go to work (especially defensively). But I don't think it means there's nothing that could be improved within the game in this regard, especially if that stuff about the "game types" is/was/still is true. That stuff needs to go. The "game type" should happen organically based on the flow of the game. Not like a "global modifier" to all players.