I think it is a combination of three things as to why the Anakin Skywalker character kills the PT movies:
-Hayden is a not an awful actor, but he is not a good one either. His delivery of whatever he says is flat and unconvincing, and I guarantee if he weren't a good looking guy, he wouldn't even be an actor. Lucas needed a great actor cause he had to carry all these dramatic moments for everyone to feel his tragedy. A great actor is able to seize on dramatic moments to cement themselves in the role, and Hayden didn't do it once in AOTC/ROTS.
-Lucas dialogue and direction were pretty poor, and that is because he is making a tragic dramatic story of this character in the realm of a 1930's cheesy serials he grew up with, and the two don't mix! If you watch those Flash Gordon serials Lucas & Spielberg loved, they didn't have any dramatic moments and they didn't flesh out any characters the way the PT did with Anakin, so it comes off as......cheesy, just the way Lucas wanted it.
-The Anakin character was never sympathetic or even cool from the first minute of AOTC. He should have been this cool ass cocky jedi who was cool under pressure and the audience would want to be like him, so when he finally becomes that tragic figure because of his arrogance, you could relate to him. The problem was Lucas made him a whiny, stalker-like, misfit, who turned out to be a prick in many ways and I ended up rooting for Kenobi to kick his ass in ROTS!