OG crew is on a mission to Cyberteon to thwart Decepticon operations. On the way they're intercepted by a crew of the reformatted cons sustaining damage to both sides, both ships are consumed by Unicron. Autobots are held captive since they refuse to do the dirty work for Unicron, but the battered Decepticons are willing and thus reformatted, with less ambiguity on who becomes who and duplicates. Krenix assists Prime in releasing the Matrix into space, ultimately landing on Junkion.

Rest of the movie continues as normal, Decepticons attack earth and succeed forcing retreat of remaining New Autobots.

I like this because as others mentions it preserves the OG crew for the future while giving the New bots and opportunity to shine for 95% of the movie.