This is just an idea. What they should have done with the Fallen is after the Sunharvester is destroyed he leaves Megatron by himself to die, which pisses Megatron off... So in.the sixth film, the Fallen could return with Unicron (they join forces) to finally kill Prime and destroy the earth, but Galvatron (who has Megatron's memories) recognises The Fallen and wants his revenge for leaving him to die. So then we'll get Optimus and Galvatron vs The Fallen (which leads to the Fallen dying) then have unicron take over Galvatron's spark/body, so we'll get Optimus vs Galvatron (which leads Galvatron to be badly damaged) then we'll have all the Autobots vs unicron! Optimus destroys unicron, and when everyone is happy cheering, Galvatron gets a cheap shot at Optimus which kills him. Then Bumblebee finishes off Galvatron! The Fallen is too strong of a villain to be in.the second film of a (possibly) 6 film franchise. It's kind of random as well.
The trouble is, that these films weren't planned as a series. When ROTF was being produced there wasn't really any thought about a 3rd film, let alone a fifth or sixth. It's only now that they're actually able to think ahead and plant seeds for future films.
Was about to post pretty much the same thing. They're conceived as such separate stories, with some new piece of lore being explored every time. It would have minimized all the conflicts and convoluted plotlines if they had been able to map out everything they would do throughout a series of films from day one. Like in comic books, where story arcs are conceived and prepared as far back as years in advance. The Marvel movies as well apparently have their future mapped out for a decade or more. I realize the next movie is never a certainty, but it's so beneficial to map out your fictional world's future rather than making it up on the fly, even if those stories never end up getting told. It seems AOE is finally starting to do that, so hopefully it only gets better from here.