Where was my catastrophic failure of the Matrix? I was promised a catastrophic failure of the Matrix! (What we got instead seemed like an anomaly, and not at all what was threatened at the end of act 2)
Where were my cryptic plot threads for me to endlessly speculate on? I immediately wanted to re-watch #2 so that I could try to understand more details. When I watched 2 for the first time, I had a lot of fun trying to put together mysterious elements on the fly. I pretty much want to re-watch 3 just because I liked the fight for Zion. And to catch a three minute gap I missed at the beginning.
Why did this feel like they dumbed it down because of the reaction to 2? If they'd shifted half the cryptic content over from 2 into 3, and half the straight ahead gusto into 2, then we would have been rockin'.
Unresolved elements: why Neo's powers still worked, the nature of the previous iterations of the Matrix, who the previous Ones were, how they differed, who the mother of the Matrix was (Architect's dismissive "Please" argued against Oracle, but Persephone -- only other major contender -- gets like six seconds of screen time), why don't we get more Merovingian and Persephone, etc etc etc. Discuss.
Ultimately I feel like if I view it as a stand-alone action flick it has one of the greatest bar none sci-fi war sequences EVER. And some other great fight scenes. But as a resolution for what the previous two films set up, it falls -- inevitably -- flat.