Pokemon/Ghost in the Shell: Stand Alone Complex.
So I don't know if I actually want to see this, or just see how cracktacular it would be. Perhaps Digimon would be more appropriate?
Actually, what I'd really like is a Battling Pet Monsters show or game that is written and plotted with appealing to the older portion of the fanbase in mind. Something with more complexity of plot, character, and morality. If the later seasons of Nanoha could do it for the Magical Girl genre, the somebody else can do it for A Boy And His Magical Electric Rodent.
I'd probably settle for a quality rendition of a battling pet monster RPG. I've never seen a complete Pokemon d20 conversion, I'm not really keen on BESM so Cock-Fighting Seizure Monsters is out, Pokethulhu is hilariously excellent (and uses sinister dodecahedrons, bonus!) but I'd like something with a bit more crunch and meat to it. Monsters and Other Childish Things has some fun gaming potential, especially if you wanted to slant it heavily back towards the Mythos side of things, but it's a bit too far distant from the Pokemon concept.
Meh. Maybe I'll kludge together something with FATE/Spirit of the Century. Right after the Avatar: The Last Airbender conversion. Or learning how to run the base game.
*ponders setting a Pokemon game in a pulptastic Spirit of the Century-esque setting*
...I should probably stop posting now before I derail the thread any further. I'll undoubtedly be back later with more Crossovers That Should Not Be.