Just a thought, but you know, I’ve always wondered, why did they never do something like a crossover between Ghost in the Shell or The Matrix? I have this funny image of Major Kusanagi sitting on the shoulder of Optimus Prime with a data cable running between them, exchanging some thoughts on how Batou and Ratchet are quirky people. (Okay, so I know the real reason–different scifi subgenres, and totally different audiences) but I really think something like that would be cool.
And while we’re on the subject, something else that might be cool, is seeing what would happen if Autobots and humanity merged to become one new race, both mechanical and biological. Maybe that would be the Maximals of the future, and then they would end up crashing backwards in time and seeing the Autobots take down the Decepticons once and for all, while trying to stay out of the way and not influence the timeline. Kinda like Star Trek: First Contact. Only with giant transforming robots and little transforming robots.
Ah, who am I kidding. These things are way too cerebral for Transformers. But it would be so cool!