My wishful 'head canon' based mostly on the desire for story and catalogue consistency is as follows:

- Skywarp becomes Cyclonus and Thundercracker becomes Scourge. There is no 'Armada'.
- Reflector becomes The Sweeps.
- The Insecticons were never that damaged in the battle and partake in the argument over who should rule. They say they will support whichever candidate can offer them the most energon.
- Back at the start of the battle of Autobot City we see Utra Magnus give Skyfire the order to get the humans to safety. Chip, Sparkplug and Carly are all seen getting into that great hunk-o-plane and flying off.
- In the post-battle tidying scene we see various characters corresponding to 1985 Autobot Cars milling about shifting city debris. It is galling to think that any toy or character should last only one year - they were due a minimum of two dammit!
- Snarl is seen in every scene in which the Dinobots appear.

I could go on but think I'm widening the topic too much.