I hope to eventually see one reboot, hopefully with no crude jokes. I think humans can have a big role, but it shouldn't be "everymen" like Shia or an out of luck family, if anything, the militar should be the ones getting the spotlight.
I would plan it as a trilogy:
Transformers: More Than Meets the Eye
This would start the same way as the cartoon, pretty much like The Man of Steel. tTe Decepticon need Energon, the war continues on Earth after they wake up and Megatron is defeated. The focus would be more on the transformers, and we should get to see more depth when it comes to Optimus Prime and Megatron. The final battle would be on space and result in Megatron's "death"
Transformers: Reign of Starscream
The battle continues as the Decepticon are now lead by Starscream, Shockwave could appear and they could state that Cybertron was destroyed a long time ago. Dinobots and Insepticon are featured.
Transformers: The Final Battle
Megatron returns as Galvatron, Unicron comes to destroy earth. Optimus Prime sacrífices himself in order to save them.
G.I.Joe should suffer a reboot too, this time being more militar with less super heroics, as Cobra Commander would be mysterious and more like a traditional terrorista.
Then down the line both franchises could crossover.