OK guy's this'll be a long one:
Have the movie start off with Starscream returning to Cybertron in search of his aerial division (thundercracker, skywarp, cyclonis, and blitzwing)
He summons them to return to earth to get revenge on the autobots or reclaim the missing allspark piece which has some importance of some kind.
While detailing his plan to his minions, unbeknownst to starscream is covert agent Ravage. With some help from lazerbeak he returns to Moon base 1 where Soundwave and Shockwave are leading the last "known" decepticons (Tidal wave and the Constructicons (minus bonecrusher, when they go to earth they reformat him into a construction vehicle). After hearing of starscreams insurrection towards Megatron they decide to discontinue their current battle with the last "known" remaining autobots on Moon Base 2 and stomp out starscream before he attains ultimate power over the Decepticons.
Meanwhile the autobots are resting peacefully on Earth living out day to day life, until they receive a distress call from moonbase 1 saying that the autobots are helpless against the decepticons lead by Shockwave. Bumblebee, ratchet, and sam head to cybertron (because sam wanted to see cybertron) with some help from Earth's government. This however is a trap set by soundwave to seperate the earth's autobots and catch them unawares on moonbase 1.
Meanwhile however on moonbase 2 where the Real last "known" remaining autobots(Ultra magnus, hot rod, hound, prowl, arcee [maybe] and mirage) are, they pick up optimus' transmission(from the end of part 1) as well as Soundwave's false transmission and send Ultra magnus, hot rod, arcee, and hound to earth to back up the autobots on earth against the oncoming forces.
Soundwave (with lazerbeak and ravage) lands on earth with the constructicons and Tidal wave. Soundwave and his tiny cohorts are sent to infiltrate the autobots base (which can be wherever), the constructicons reformat bonecrusher back into one of them and they become construction vehicles, and tidalwave is sent to get Megatron at the bottom of the sea.
Starscream and his followers find agent simmons who has been fired in disgrace and decide that they will need some kind of human help in order to successfully vanquish the autobots for good. They can also do other stuff too I guess.
Over on moon base 1 sam and his autobot companions find out it's a trap and have to fight off shockwave and his many drones, when all seems lost mirage and prowl show up to save them barely escaping from shockwaves deadly cannon form (like the one in the video game). From there they retreat to moon base 2, and sam learns a great deal more about the autobots and the decepticons.
On earth there is now general conflict between Ultra mangnus and Prime. Through the years of warfare and the continuous loss of his comrades has made Ultra Magnus extremely cold towards everyone sometimes even his own troops. There is a power struggle between him and Optimus leading into a fight (the first sign of the reality of war between characters).
Mikaela meets Arcee obviously and they hit it off.
It all boils down to Megatron coming back with some kind of new power due to the allspark and ending with a huge cliffhanger like most sequels do nowadays.
What I wan't to see though is some real character emotion between not only the autobots, but the decepticons as well. In the last movie they were just scary bad guys who grunted a lot, this time I wan't to see some real interaction. Have the constructicons despise the war and megatrons ideals. After all in the beginning the constructicons were actually good scientists until megatron corrupted them with thoughts of power and evil. Have tidal wave fight the autobots and when all seems lost the constructicons would combine and fight the enormous Tidal wave. Sure it would look like a crappy Godzilla fight, but who else could take on a being that monstrous? He'll obviously destroy tidal wave, but just as he has assured victory megatron will (somehow) kill him for treachery. He'll die and the autobots will remember his honorable decision to fight for what you truly believe in (awww a message to the kids).
I have also stressed this one idea through many of my posts and that is to have Starscream fight megatron in an aerial battle over the ocean while the navy and airforce try to take them both out in the process. They could use the aircraft carriers as mini islands to land on and fight both verbally and physically (fists and weapons).
WHEW
that was long.
so what cha think
I'm open to
flames/comments/ideas/changes