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Most likely, as the Decipticon general Megatron and his lieutenant StarScream both escaped, assumably back to the Nemesis. Soundwave also survived, although he was in no actual combat in the movie. There are also untold numbers of Decipticons still lurking aboard the Nemesis as well as the "hatchlings" that are briefly mentioned during the film.
I would assume the 3rd movie would incorporate Unicron, the ultimate-evil planet-sized transformer.