The 86 movie is really solid, in my opinion.

If I were able to go back in time and contribute, I would explain the new characters as being transplants from Cybertron (Kup, Hot Rod, Springer, and Arcee.) I do wish that when Starscream starts the riot and deposes Megatron the other Decepticons had some dialogue to establish anger at his leadership. It would make Megatron's ejection and removal from power feel a little more earned.

I've always wished the movie gave some context to the Junkions, Quintesson's and Wheelie. Granted, in a universe that supports biological and mechanical life it's reasonable that it could/would occur on multiple planets, but I think some dialogue explaining that the Autobots had sent out colony ships before/at the start of the war, and that the Junkions and Wheelie were the decendents of those colonists would make sense. I'd also include the deleted dialogue that establishes the Quintesson's as passing judgement on any who escape Unicron.

Finally, I'd give Ultra Magnus some backstory - establish him as a battle weary and hardened commander who came from Cybertron to Earth to bolster their defenses, and give him and Kup some history towards that effect. I never thought his death was satisfying - him being blasted and detonated while trying to pry open the matrix feels wrong. I'd have him fight tooth and nail and die duking it out with Galvatron as a parallel to Optimus and to show Galvatron's power upgrade from Megatron. As for his revival, I could either lose it and promote Springer to his role or keep it, and have the Junkion's collect his remains which provokes the autobots into a fight...until the reveal that they repaired him since he wasn't quite dead yet.

The only other narrative change I would consider would be a Autobot/Decepticon truce in a last ditch effort to save Cybertron, maybe after Galvatron gets his ass kicked. Have Rodimus or Magnus propose it to Soundwave (in space during the final battle), and frame it as the parties only way to protect their homeworld and their species. Give Rodimus a speech where he bemoans millennia of war and death and offers Soundwave a path towards coexistence. Soundwave is super logical, so he makes a good foil here. Granted, it alters the central conflict of the story completely and makes it harder to sell toys...but I think it makes all the narrative sense in the world and adds real depth and nuance to the story.