I am going to put these in list form because it's easier than a long treatise
1. I feel it was much, much too easy for the Doctor to get out of the Pandorica. Come on, all those locks, all those time-keys and crazy bonds on the thing, and all it took was a bleep and a shiny from the screwdriver? I don't mind a little fantasy in there, but the thing is just a magic wand and it makes no sense. Did none of the Evil Alien Brigade think: "Perhaps we should make it impervious to the only tool the Doctor ever carries? No? Too expensive? Johnson out sick this week? Never mind..."
2. I'm still not clear on why Amy's house was "too big" or who made it that way. Can anyone help me out on this? I get that possibly Leadworth was not as exciting a plot point as many of us hoped it would be, but they ragged on about that house endlessly and I still don't get it. What was the purpose of that, and who did it? And I've heard it was just that that was too big a house for Amy and an aunt but I feel that's a bit judgey on the Doctor's part, saying all these cryptic things because in his opinion the house was a bit upclass for Aunt Sharon? Maybe Aunt Sharon had kids who've moved away, or she likes to do a lot of crafty stuff, or she's sunk in a subprime mortgage because she bit off more than she could chew. Dude, he was in the house for like five minutes, so if that's the answer? It's a little dumb and prosaic for how much they built it up.
3. So this new Rory is human Rory and not Plastic Rory, who I liked a lot better than human Rory generally. Seems like a bit of a shit deal for Waiting Rory--but I suppose it's possible that we'll find out next season that he has Waiting Rory's memories or something. Here's hoping there's some interesting PTSD there, or the whole "it'll drive you mad" thing was a little silly.
4. River, River, River. Honestly, I feel that this is a case of bad casting. I don't like Kingston's portrayal of what is essentially Jack with breasts and frizzy hair. She's rather one or two note, and I get no sense of depth of the character from her. I liked the last scene with her saying everything would change--that was the very first time I liked the character. It did pop into my head once more that she's the Doctor, down the timeline. Oh, how I'd love a female Doctor! But still, the my love and sweetie and all that is super annoying, especially having to hear it three times in a row, and dude, "hello sweetie" is a terrible catchphrase. Also, how did she still remember the Doctor and have the Tardis shaped book when there had never even been a Tardis until Amy did her thing? Which wasn't a thing she did? So much as thinking really hard--because if he never existed, why should a blue book make you think of anything in particular? What was it that allowed them to remember?
5. I loved Smith's monologue by her bedside. It was lovely. Much better than Ten's departure and whining.
6. I do feel there's a bit too much handwaving as to this solution. She remembers...and that affects the universe how? Because she had the universe poured into her head. What does that mean? She can manifest anything she remembers, or only lead actors? I am all for the value of a good story, but as with The Lodger, I am at a loss to understand how emotions affect machinery, no matter how powerful the emotions. It just feels a bit lazy to me.
7. I agree with another poster here that it was a bit of a narrative cheat to wink out the earth in the last moments of TPO, and in the last moments of the previouslys, only to have it be not winked out in the POV of the episode, nor addressed. That's not quite fair. The earth was gone, everything was silent. Eye of the storm, yes, but we saw the earth go, and if they weren't going to make a thing of it, they should have ended TPO a split second before it disappeared.
8. I've seen a lot of people say that the episode is perfect. I think we all get a little excited right after a finale--people said that about the S4 finale, which I thought was one of the worst things ever to air on television. Perfect is a little much--this was no Blink or The Doctor Dances or even for my money a Parting of the Ways. It was an acceptable conclusion that didn't take many risks. My Faith in Moffat is not been hit by a ray of Pandorica Light and perfectly restored. It was pretty good, but the season was still generally weak, and I would much rather have seen something darker and more interesting with regards to Amy (we discovered nothing in this episode we did not already know about her, it's all chalked up to a vague "special" and not addressed further) and Leadworth and the construct thing--but it was a nice feel-good episode where I didn't really feel much of a threat most of the time. Whereas I was on the edge of my seat in The Pandorica Opens. It certainly doesn't fall flat like so many of RTD's two and three parters, but it sort of fell...crooked, to me. Maybe I'm just still not connecting to Amy as a character, and therefore can't get excited about her specialness, which we are constantly told about but never really shown. (I do like that there will be a trio in the Tardis next season, and I like Rory, though Amy still treats him like crap and brushes him off most of the time, never behaving like someone in love unless she's aimed at the Doctor, even at her wedding to said object of some fairly anemic affection, and not even refraining from rolling her eyes and snapping at him right after he waited 2000 years for her. Amy remains somewhat unpleasant, and the Doctor too, what with telling someone, usually Amy to shut up at least once an episode--my new drinking game. At the same time, some of the fan adoration of Rory and simultaneous hatred of Amy makes me uncomfortable, as it smacks of hating on the girl for speaking out of her place, and loving the boy no matter his faults.) Maybe I just read the Doctor Who LJ community too much, so the backward-traveling Jacket!Doctor wasn't a surprise stroke of genius but something I took for granted all along because we all figured it out with a million screencaps from clever viewers. I just felt that not too much really made actual sense here, from the very first scene of popping the Pandorica like a box of jelly babies to magical memories somehow making everything perfect at the end. Deus ex Amy.
9. The Tardis is, was, and always shall be my favorite character on this show. I never wanted the Doctor to come for me. I wanted the Tardis to show up on my doorstep, glowing blue and beautiful and full of promise.