If I could just stay off for a little bit, I don't think "killing Anakin" is a good idea at all. I think it goes to the root of the prequel concept. If you make it seem like you've really killed Anakin, sure it would be a big twist that Vader is Luke father, but there will be two major problems.

One - "wait, what? Anakin was definitely dead. There's no way Vader's telling the truth. Well I guess I'll have to turn on ROTJ and find out what happened..... hmm, I just watched ROTJ and they didn't explain it at all. I'm very confused."

Two - one of the reasons why the twist in ESB was such a shocker was because we were lead to believe that Anakin was a great jedi. We desperately want Luke to be as good. Then we find out Anakin was not a good jedi, and we are completely blown away. But if we already knew that Anakin turned to the dark side, the twist is diluted.

My solution for these - fixing number one is simple. Show that Anakin turned into Vader! I think it should be shown in full in ROTS. But, and here is how this post is on topic, you could, if you wanted to, have a flashback to Anakin being saved and turned into Vader in ROTJ.

My solution to number two - actually there isn't really one from an editing stand point. That doesn't mean there isn't a solution. I firmly believe the saga should be viewed 4-5-6-1-2-3 (though 4-5-1-2-3-6 works to). I think a prequel is intended to show what came before. These prequels were made to show how Anakin became Vader. If you take that out, there's not much of a point.

(And to just bring it back to Padme dying for a sec, what I'm trying to say is, why would you take one of the better aspects out of a film that you are trying to make better? When you could easily take out a small line from another film (a change that would not hurt that film I would like to point out)?