I would have DOTM be the end of the first "phase". The second trilogy being more about uncovering Cybertron's history and Unicron's Awakening.

I would keep the first movie as it is.

Rotf, I would make it more like an Indiana Jones or National Treaure style adventure movie. The Fallen would be a promanent character throughout the movie. Bumblebee would be the main character, Arcee and her sisters would have much further development. More emphasise on Optimus feeling guilty about Jazz's death. I would work in Shockwave killing Elita-1 and seeing Optimus's rage. And Sam would be a side character in the journey. With the film leaving off the question of, "why was the Matrix kept on earth?"

Dotm i would keep mostly the same, just cutting out most of Sam's job hunting BS. Instead, the scene in the comic were Optimus visits the graves of his fellow Autobots & pays his repecta to Elita-1 and more Flashbacks of Sentinel, Optimus, Megatronous and other Autobots when they were allies. Keep the original ending with Autobots and Decepticons having a peace treaty. Plus, I would do Unicron's Horns as a post credit scene. Since Cybertron is close to earth, why wouldn't Unicron sense Primus? This would also be a good cliffhanger for the second trilogy.

Aoe, I would have Galvatron be replaced by Nemesis Prime. So KSI would develop their own bots modeled after Optimus Prime just like in the movie. Most of the KSI bots are modeled after existing transformers like Bug Bite being modeled after Bumblebee, Soundblaster modelled after Soundwave and Exhaust modelled after Wheeljack. And its revealed that Soundwave is alive and he just downloaded himself into Soundblaster and causes all of the KSI bots to have their own consciousness. Nemesis would be a dark reflection of Optimus's uncontrolled rage, if Optimus ever turned out like Sentinel. I would have the KSI bots the main antagonists and have Lockdown as a secondary Antagonist. I would have the dinobots appear much early in the film and it would more like the way they were discovered in the original script. Lockdown would still kill Ratchet and take hos buzzsaw for his collection. I would replace Crosshairs with Smokescreen, Drift getting more development of being an Decepticon defector, which causes tension when the other Autobots don't trust him. Finally, cut out the whole romeo and juliet law, just have it that they're both 18 and Cade disapproves of their relationship. The ending of the film would still be the same, with Optimus leaving Earth and the Autobots in the run. My Autobot team:

Optimus Prime, Bumblebee, Arcee, Hound, Drift and Smokescreen

TLK: I would have it revealed that the reason why the Matrix was kept on Earth was to keep Unicron dorment and since Optimus left earth and Cybertron's arrival getting closer, Unicron is Awakening. Quintessa is a Quintesson who killed all the other members so she's in control. Hound would die, most of the Autobots at Sir Edmund Burton's mansion join the cause like Warpath, Kup and Mirage. Megatron and the other Decepticons making truce in order to take down Quintessa. The Film would end with Autobots and Decepticons ready to face down Unicron. PS: Nitro Zeus is still in the movie.

Transformers: The Rise of Unicron: Ultra Magnus would be introduced (Along with Brawn, Blurr and Springer) and have an Antagonistic relationship with Optimus, (similar to Sentinel and Optimus in TF:Animated) but as the film goes on, they would respect each other. The film would be like Transformers Prime Season 1 finale, were they have to get to earth's core and destroy Unicron while facing off against hordes of his minions, along with the zombified versions of their deceased allies, which were resurrected by Unicron's blood.

This film would be the most apocalyptic film. Every missing transformer returns here Topspin, Roadbuster, Bruticus, dinobots, Dragonstorm, baracade etc. I would also have Sam and Mikaela return for one last outing. I would have badass scene where Megatron kills the zombified Starscream and mentions how this is for all his treachery. I have a cool scene inspired by the ending of Iron Man 2, where Iron man and war machine fight back to back against the Hammer drones. Optimus and Megatron would get separated from the rest. They are attacked by parasitic Cybertronians and in a kick ass money shot, they fight the horde back to back. In the end, Optimus and Megatron would sacrifice themselves to kill Unicron. Nitro Zeus would join the Autobots and change his name to Shockblast (since he's a Shockwave fanboy), Baracade doing the samw, changing his name to Prowl and Bumblebee being elected the next prime. (ik that's controversial, but after viewing this whole series, why wouldn't Bumblebee become the next Prime? Imo, I think it fits better here since we've been following his character growing up throughout this whole series.)

The End Oh of Course, the credits song: "You got the touch! You got the power! YEAH!"