Ooh, a project.

Well it would be a trilogy, like you said.
The first movie would include the following 'Bots and 'Cons. (Deaths are marked with a *T*)

Optimus Prime
Bumblebee
Ironhide
Ratchet
Huffer *T*
Windcharger *T*
Cliffjumper
Brawn
Prowl

Megatron
Starscream
Soundwave
Rumble
Frenzy *T*
Ravage *T*
Laserbeak
All 6 Original Constructicons
Thundercracker *T*
Skywarp *T*
Plot:
The Autobots come to Earth searching for Energon to fuel their ongoing journey to find the Decepticons, who had recently fleed to an unknown location. Little did they know that the Decepticons were on Earth. When Bumblebee meets a young human named Spike (Jake T. Austin), Optimus realizes (after engaging in a deep battle with the Decepticons) that they cannot leave the planet until the Decepticons are fully defeated.
The Second Movie would include the following 'Bots and 'Cons, following the same rule

Optimus Prime
Bumblebee
Ironhide
Ratchet
Sideswipe
Sunstreaker *T*
Jazz *T*
Cliffjumper
Brawn *T*
Grapple
Tracks
Mirage

Megatron *T*
Starscream
Shockwave
Soundwave
Rumble *T*
Laserbeak
Buzzsaw *T*
All 6 Original Constructicons
Barricade
All 3 Original Insecticons
All 5 Original Stunticons *T*
Scourge
Cyclonus
PlotThe Decepticons are now looking for a small sphere called the Power Core, which could fuel a machine large enough to destroy the Earth's sun. Meanwhile the Autobots are now protecting Spike (Jake T. Austin) and Carly (Some 16 year old girl...) from Barricade, a Decepticon out to destroy Bumblebee. After the defeat of many of the Decepticons, Optimus Prime now realizes that their new hom is on Earth.
The third movie would be the final installment.

Optimus Prime *T*
Aerialbot Powered Optimus Prime
All 5 Original Aerialbots *T*
Bumblebee *T*
Goldbug
Ironhide *T*
Ratchet *T*
Sideswipe *T*
Sunstreaker
Hot Rod
Ultra Magnus
Blurr
Springer
Inferno
Grapple *T*
Tracks *T*
Warpath
Hound

Galvatron *T*
Starscream *T*
Soundwave *T*
Rumble *T*
Shockwave *T*
Ratbat
Laserbeak (minor role)
Scorponok *T*
Blackout
Sideways
Ransack *T*
Scourge *T*
Cyclonus
PlotOptimus Prime is killed by Galvatron and his new Decepticons, however, Ultra Magnus takes over as leader and the Autobots travel to distant worlds where the Decepticons are causing havoc. Spike (Ashton Kutcher) and Carly (Ashley Tisdale) are now married and have a kid, Daniel (Some 14 year old boy), whom stows away on the Autobot Ship. After plenty of Autobots and Decepticons die, and the Autobots make an alliance with the Aerialbots, the Aerialbots soon die to power up Optimus Prime, as he and Galvatron engage in one last final battle.
Thy wall of text is complete >_<