Personally I think the folks who are so adamant that this ISN'T in reference to The Fallen of the comics are simply the people who, prior to this news getting out, had never personally heard of The Fallen. The reasoning is something like this:
"I have not heard of The Fallen, ergo The Fallen is obscure, ergo they wouldn't use him in a movie," which is obviously faulty logic."
Personally, I would be pretty effing surprised if it WASN'T The Fallen.
a.) The Fallen is the next logical step in the trilogy. Start with Megatron, ramp it up to The Fallen, and eventually to Unicron in Transformers 3. (Of course, methinks that we'll be seeing Megatron again, too)
b.) All the talk about this movie is that it's going to be absolutely epic in scope, that it'll blow the first one out of the water in that regards. How, pray tell, do you accomplish that with the same villains and the same stakes?
c.) Revenge of the Fallen, despite it's generic sound, isn't a title that just fell into their laps. They had to consciously choose this title. Picking a generic title that just happens to include the name of a pretty key villain would just be sloppy, and I hope they'd know better than that. If you're just going for a generic title indicating the return of the Decepticons, you could just as easily (more easily, even) come up with something that doesn't have the name of a key figure in it. That'd be like calling the next Batman movie The Dark Knight Returns. Yeah, in theory, they could, and it could just be a generic title, but it'd be sloppy to do that considering that it's already a title of significance.