Though it definitely didn't live up to its potential, I don't think that this was due to the killing. I think that this movie was a victim of its own ambition. Looking through it, I see one for Angel, one for Jean/Scott/Wolverine, one for Bobby/Kitty/Rogue, and one for the cure. All of these should have been better developed. For example, they had 5 scenes with Angel in them at all. One when he was cutting off his wings, one when he was about to get the cure, one when he entered the mansion, one when he left, and one when he caught his father. Three of these scenes are 30 seconds or less. This is not even close to the proper amount of time that it would take to develop a character. (On a sidenote, I didn't like that they tried to make him an angsty teen, either. As far as I know, that was never how he was portrayed in the comics or the cartoons. However, since they portrayed a lot of things unlike they were in the comics, and not all of them were bad changes, this is only my opinion.)
Another complaint I have commonly heard is that there were a lot of people out of character. There were three that I think were, in fact, out of character; Magneto, Xavier, and Pyro. I don't think that Magneto would have abandoned Mystique so easily, even though she appeared to be normal. It didn't cross his mind that she there might be a counter to the poison in the darts? And even if there weren't, is Magneto so completely ruthless toward humans that he would abandon one that was not only formerly a mutant, but that had saved him from becoming a human? If so, then why didn't he kill the family in the car on the bridge? As for Xavier, he would never have said something so callous as "I don't have to explain myself to you." His character, when it came to dealing with Jean, was completely displaced. As for Pyro, the complaint I have against him is more minor. He was friends, of sorts, with Bobby and Rogue, in X2. Yes, their relationship was somewhat uneasy, and it was strained by their disagreements, but still, they were friends. And, he was never so hostile toward Xavier as he seemed to be in this movie. Both of these can be somewhat accounted for by his closeness to Magneto, but since Magneto was friends with Xavier, I have a hard time believing that Pyro would try to curry favor with Magneto by threatening Xavier's life. And I have an even harder time believing that he would be so eager to kill Bobby, considering they were on decent terms at the end of the last movie.