A long time ago, I wrote the first part of a fan-fic that was a crossover of Pokemon and Beast Wars: Transformers. Working with the anime, the story was as such: set during the first season (I wrote it back before Gen 3 was announced), the Axalon and the Darksyde transwarp into orbit over the Pokemon world, trade shots, and crash planet-side, with the Axalon landing in Grandpa Canyon (where "Attack of the Prehistoric Pokemon" took place) and the Darksyde crashing into Cinnabar Island, obliterating the volcano and damaging most of the island (Team Rocket was also there, they survived). As Ash, Misty and Brock went to investigate the canyon, the Maximals and Predacons assessed their situations and scanned beast modes from the local Pokemon. Team Rocket is caught by the Predacons as they try to sneak in for a closer look, but are spared by the discovery of the Maximals' crash site and Megatron ordering everyone to attack. It ended with Ash and friends trapped between the two factions as they prepared to battle. Never continued it, though.

Anyway, if there was an official Pokemon/Transformers crossover, which Transformers would you like to see get what Pokemon as alternate modes?