Microsoft Game Studios: Instead of a RPG, a M-rated shooter with bullets, blood and breasts. A 17-point achievement for catching a shiny Pidgey ("Memetic Mutation"). Event Pokemon available for 240 Allards instead of being distributed for free over wi-fi.
Sony: 3-D graphics out the ying-yang because 2D is for suckers. You'd have to take out a second job to pay for stat drugs in game. The games would come on a proprietary format and Spiderman would be in the Elite 4. Kingler kept out of high-level play after everything attacks the weak... nah, too easy.
EA: Although the games would stay as they were (except maybe a PC port), Pokemon Stadium would be released every year. As a side effect, the announcer would provide such salient advice as "If you hit the Pokemon, they lose hit points".
Activision: If they actually bothered to release it because GameFreak wouldn't allow it to be
Valve: Although the games would be high quality, Valve's perpetual development cycle would mean we'd be anticipating Pokemon Crystal's release in 2009.
Ubisoft: The two versions would consist of Tom Clancy's Pocket Monsters and Assassin's Monsters, both games requiring massive amounts of unnecessary stealth to complete. The third version? Imagine: Mudkipz.
Capcom: Pokemon Diamond: Championship Edition. Search your hearts, you know it to be true. And every starter would learn Sketch 8 times per game.
SquareEnix: Nomura takes over NPC design to ensure proper amount of belts and zippers. Red and Green re-released on every platform known to man.
Atlus: Level cap raised to 9999, Arceus available as a bonus boss after beating the game except its base HP is 1 billion. May's chest swells even further. Instead of evolving by level up, trade, etc Pokemon evolve by the trainer pulling out a gun and SHOOTING THEM IN THE HEAD.
Bethesda: A first-person RPG where NPCs now have voice acting. Despite using approximately five voice actors for the whole game, all is forgiven by the community after Professor Oak is voiced by Liam Neeson or Samuel L. Jackson. No Mutants Allowed threatens a boycott because Nintendo isn't publishing it, but eventually folds like a cheap suit.
SNK: Champion's party has 6 L100 max stat Pokemon. Chosen from the ingame legendaries. May be dual-published with Capcom.
PopCap: You thought Pokemon was addictive before...