Transformers writer Roberto Orci confirmed that Megatron returns in Transformers 2. His exact quotes are "Megatron returns!...Keep it quiet". I guess this is big news but then the Voyager class toy packaging gave this away already.
What still confuses me is Michael Bay saying Megatron doesn't return. If he said it to fan sites, you can file it under intentional misdirection. However, he apparently said that (love a direct quote to verify) to Empire Magazine and as general rule of thumb it is a bad idea to "misdirect" the press. I get the feeling that both are telling the truth as part of the storyline. Time will tell. Thanks to Michael for the link.