Adventures through space (Transformers Exiles)
Crashed Ark on Prehistoric Earth (Beast Wars)
The bots and cons awakening in 1984 (G1)
Other
Beast Wars sounds interesting, but rather than explicitly tying it to the old Beast Wars cartoon, why not have the characters from FOC crash land on prehistoric Earth, take on beast modes, and continue fighting from there? That way you avoid any weird time travel plot points, don't delve too deep into continuity the casual player won't follow, and at the end of the game you can have the two factions all rendered offline, setting up a resurrection in 1984 or 201X for the next game.
Ugh! If they went with the Beast Wars idea I would be so disappointed. Realistically they would have to go with the Velocitron, Junkion and lost in space following the matrix's guidance.