There were a bunch of things I didn't like about AoU but I'll start with my top three:
1. Too many damn quips that made the movie feel more like a running punchline than anything serious. Not that I wanted something DC-serious like TDK, but geez it seems like the majority of Marvel's movies just can't find the right tone and end up feeling like there's never any "dramatic weight" for lack of a better term. TWS got it right, I want more movies with that kind of tone!
2. I'm really, really tired of seeing the Avengers fight amongst themselves. I don't care what the reason is, it's just plain old and I'd prefer seeing the Avengers fight villains instead of each other. If Civil War is just going to be more Avengers in-fighting then I think I'm going to pass.
3. The fighting in the action setpieces was just....uninspiring, and there was no sense of anything bad that could happen, like someone geting hurt or killed (well until Quicksilver got randomly offed). I mean, in TWS, there were points at which I thought either Cap or BW could die at the hands of WS. I got none of that from AoU, and was pretty much convinced that everyone would make it out alive and easily at that. I can buy that characters like Thor, Vision, Iron Man, and Hulk could easily tear through tons of Ultron bots, but the other members of the team (Cap, Hawkeye, BW) should've had to put way more obvious effort in, and should've gotten either tired or injured, or both.