Originally, I said Unicron, but after T2, I say just Megatron. An entire film of Megatron cut loose with, of course, Starscream stabbing him in the back constantly. The Fallen's presence created a lack of Megatron's threat level, so Bay should work it back up.
You know what would also rock? An adaption of the Time Wars. Introduce Galvatron and Rodimus Prime through a time loop.
AUTOBOTS
Optimus Prime
Bumblebee
Ironhide
Arcee
Chromia
Ratchet
Skids(dies)
Mudflap(dies)
Elita-1(dies)(sacrifices herself near the end of the movie)
Sideswipe
Jolt(dies)
Wheelie
Kup(dies)
Sunstreaker
Wheeljack
Blurr
Cliffjumper
Ultra Magnus
Alpha Trion(cameo)
Blaster
DECEPTICONS
Megatron
Starscream
Soundwave
Shockwave
Skywarp
Thundercracker
Thrust
Rumble
Ratbat
Laserbeak
Blitzwing
Sixshot
Runamuck
Runabout
Astrotrain
Barricade
OTHERS
Dinobots(their creation, the movie ending with them being made)
Insecticons
Scourge
Cyclonus
Unicron(only by name)
seems Leo may have a bigger role...
http://www.superherohype.com/news/transformersnews.php?id=8467