That was what I thought as well - that Megatron was the 'one who had fallen', who was coming back to inflict revenge on all, not just the Autobots. It never occured to me that it referred to a character called 'The Fallen', and I think that ambiguety is what the movie people want, to surprise the general public, who would be assuming Megatron is the central element of TF2.

I also had an idea for a story which had Jazz be reanimated by Sector 7, as a bit of a rampaging zombie, inflicting revenge on everyone on behalf of Sector 7 (who were disbanded, so have scores to settle with everyone), but Jazz eventually ends up regaining his sentience and helps defeat Sector 7 once and for all.
Back in my early fan days, with heaps of spare time and enthusiasm for fanfics, I would have written that one up as a story, but now it'll probably just remain as a story idea...