First, there was the incredibly contrived situation. The Doctor randomly takes them to a planet that's quarantined with a plague but he doesn't know that. Amy pushes the wrong elevator button without asking which button to push first. The medical computers of a planet that specializes in studying other worlds can't recognize aliens. Idiot balling much?
Second, there was Self-Pitying Screwed Up Future Amy. As somebody on my Twitter feed put it: "Rory waited a thousand years for you to finish sitting in a box and never even grumbled. Suck it up, Amy!" And honestly, given what we've seen of Amy, it just didn't ring true. Who knows, maybe being put into an incredibly unlikely torture scenario for 30 years might have made her go squirrely, but given all the other crap she's put up with in the past two years, it doesn't seem likely.
Finally, there was the ending. Did anyone ever think the "two Amy Ponds" thing was going to happen? Of course not. Did anyone ever think Self-Pitying Screwed Up Future Amy would be the one who stayed? Of course not. The only question was whether she was going to be killed in battle covering Young Amy's escape, or get a tearful sacrifice death instead. So why did the episode waste so much time pretending it was important?
Finally, what did this episode achieve? Development of plot? Nope -- nothing has changed. Revelation of character? Nope -- the episode didn't tell us anything we didn't know about Amy, Rory, or the Doctor. (Remember him? He's that not-companion guy.) Rollicking adventure? Not particularly. At the end of the day, it was 45 minutes of manufactured wangst. In the words of Monty Python, "It's all been a complete waste of time."