A smaller list
For me, at least. 12 bunnies.
1. Sunstreaker realizes that the sand all around the Ark would be perfect for glass-blowing. Perhaps it’s time he took up a new artistic medium.
2. Soundwave can sense the thoughts of others, but _________ (Blaster?) can sense their emotions.
3. Some Cybertronians land on a planet with extremely low gravity, and for a short time they understand everything:
why the flying ‘Bots and ‘Cons can never stand being forced to stay on the ground for long periods of time;
why the Seekers were acting so crazy on the other planet which had such high gravity that they couldn’t fly;
and why the first Decepticons, wires singing with the joy of flight and looking down at the flightless Autobots far below, were so easily convinced of their inherent superiority.
4A. Despite common myth, Autobot and Decepticon programming is exactly identical. All Cybertronians have built in ‘morality’ programming that affects all their actions and cannot be removed. The idea that Decepticon core programming does not allow for any ethical influences is a lie, spread by the being/mech/group of mechs who captured the Decepticons as sparklings and made sure that their moral programming developed incorrectly.
4B. Even if some Decepticons did have different programming without ethical influences... could you tell which ones were true Decepticons and which ones were corrupted Autobots? In the end, is there a difference between no morals and bad morals?
5. All the work necessary to save Orion Pax and Ariel and convert them to their new forms as Autobot leaders caused Dion to be lost in the shuffle. He ended up quietly dying at a small local repair bay, when a paperwork mixup put him further back in the queue for treatment than his injuries demanded. Unable to adjust to his death, Dion returns as a ghost and ends up haunting Optimus. After all, if the future Prime hadn’t needed so much attention, then Dion - whose wounds were even more severe - might have been able to get help in time.
6. What if the Dinobots acted more ‘normally’ - proper grammar, etc. - while one of the combiner teams had the Dinobots’ quirks, mannerisms and reputation for stupidity?
7. What if more than one universe’s events all happened to the same Earth? i.e., the Ark and Nemesis are uncovered in the 80s, then more Autobots land in search of the Allspark in 2007, and fifty years after that the Animated crew arrives.
8. Terratronians, a human-sized robotic species, discover that they are not alone in the universe when two warring factions of Cybeings (a huge organic species of some sort - dragons perhaps?) crash-land on Terratron.
9. Transformers probably don’t use any form of ‘handwriting’… so, what about that old cliché that all doctors have messy writing? Do all of Ratchet’s reports have typos or something?
10. What if Sam did push the All-Spark into Optimus? (And wouldn’t Megatron just immediately squish Sam if he did that? Did Optimus realize that he was essentially murdering Sam as well as himself?)
11. Instead of being the Decepticon leader, Megatron is the Decepticon medic.
12. Someone gets sick of Skywarp’s pranks, Thundercracker’s apathy, and Starscream’s… everything. So they pull an anti-Seeker prank in the Decepticon base: narrowing all the doorways.