Here are some things that I think would make a very good My Little Pony and Transformers crossover:
1. Optimus Prime would have a lot of similarities with Twilight Sparkle:
• Both were once librarians that ascended to a title of leadership, princess and prime.
• Both were once pupils of wise predecessors; Twilight to Celestia and Optimus to Sentinel Prime.
• Both have subordinates that they view as friends.
• Both believe in peace and friendship with other living things.
2. Megatron would be a dark reflection of Starlight Glimmer:
• Starlight was once a tyrannical leader who ruled her people with an iron fist, but not too extreme like Megatron.
• Starlight was once driven by a delusional belief of equality that almost caused destruction to Equestria, almost like Megatron’s belief that tyranny brings order which has brought destruction to Cybertron.
• Both were archenemies of the main heroes, Starlight to Twilight and Megatron to Optimus.
• But the main difference is Starlight reformed and Megatron hasn’t yet and maybe never will.
3. Starscream and Rainbow Dash would become archenemies. Both are complete opposites. While Rainbow is loyal and brave, Starscream is treacherous and cowardly.
4. Fluttershy tames and befriends the Dinobots.
5. In the past, Megatron and Optimus would have once been friends until their different beliefs drove them apart and turned them into mortal enemies. Some ponies see this as a friendship problem and want to try and help rekindle the friendship between these two, but they might be way beyond that point now.
6. Twilight Sparkle would have a friendly rivalry with Perceptor, both tend to engage in a ‘science vs. magic’ debate.
7. The Wonderbolts would become friends with the Aerialbots and archenemies with the Seekers.

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Yeah. I have to say, this IS some pretty well thought-out stuff. Thanks greatly for sharing this with us. :-D