I have a few ideas:
Mario X Pokémon - This comes with two ideas. One is a platformer that has you play as Mario, Luigi, Pikachu, and Meowth to save the Pokémon world from Bowser, who has kidnapped the mirage Pokémon and Arceus, who Bowser will be riding on for the final battle. The second idea is using the formula of the mainline Pokémon games, either on an existing region or a new region, but with a twist: Mario enemies will appear on grasses, caves, and seas alongside with wild Pokémon, but they cannot be captured. The koopalings and Bowser Jr. will serve as the gym leaders, even though they're the ones who've captured the original gym leaders and taken over their buildings. Larger Mario enemies such as Petey Piranha and Glooper Blooper will be blocking your way to the next gym, and Bowser will be among them twice. The third time is where you'll have to fight him in a different form, exclusive to this crossover, after you beat his variation of the Elite Four.
Street Fighter X Pokémon - Not much else to say except a Street Fighter character will be paired with a Pokémon that fits their personality or style (Ex: Ryu and Lucario, Zangief and Ursaring, Vega and Weavile).
Mega Man X Pokémon - This is something I have to get creative on. I've already got the basic content: each Robot Master will be given a Pokémon that fits their theme, and Mega Man gets Eevee as his partner. The gameplay has to somehow combine elements of both the Classic Mega Man games and the mainline Pokémon games.