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According to Frank Welkers’ website, he has not been cast as Megatron.  The role has not been cast and he is still in the running. 

Regarding Transformers the Movie 2 (2007), everyone says you’re in it, even IMDb Pro: Transformers: Main Details » Frank Welker … Megatron (voice). I’m so confused, are you or aren’t you in it? I’ve also attached a few fan letters for you to answer when you have some free time. You’re the best! Thanks!

Doreen (2/1/2007 4:36:37 PM PST)

Hey Dor … As you can see by my responses [below], everything you’ve read at this point has been rumor and misinformation. As of this moment, to my knowledge, they have not cast Megatron and I am still very much in the running.

Frank (2/20/2007 7:51:59 AM PST)

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Hello, Mr. Welker!

You have done a great job voicing Megatron in the G1 Transformers series. I know that Peter Cullen is going to voice Optimus Prime in the new live-action movie. Are you going to participate in it? [snip] I would like to contact Peter Cullen. Do you know how?

Sincerely,
Omeed Mirhakkak

Dear Omeed,

Thanks, I really enjoyed doing that voice and playing a villain for a change. I know I have been asked a lot about the movie, but at the present time I have not been offered any roles. That doesn’t mean it’s final, they are still doing voice casting. Peter Cullen is a hard man to track down, you might try some of the “Transformer” sites and see if you can get a message to him.

Frank

Source: Frank Welker Homepage: A FRANK DISCUSSION: Fan Questions to (and Answers from) Frank Welker