Atlus
>They made Shin Megami Tensei.
>I think that a Pokemon spinoff with SMT mechanics would be really good: You must parley with other Pokemon instead of catching them. You can participate in battles too. Battles with legendaries would be far more interesting and difficult. SMT is everything that Pokemon lacks of, in my opinion.
Namco Bandai
>They made Tekken and Tales series.
>They have already developed Pokken, so they know how to work with Pokemon designs.
>Slight mechanic changes taken from fighting games would freshen the games a little (Tales fashion)
Square Enix
>They made most of the great SNES and PS1 RPGs.
>They have a lot of experience in the topic.
>Music and Graphic quality would rise a lot. It's plausible that plot and characters worsen, but there would not be much different than what is today.
PlatinumGames
>They made Okami, Bayonetta and The Wonderful 101. (Viewtiful Joe doesn't count, it was Clover back then)
>They have experience in Beat-em ups, not necessarily what Pokemon needs, but that would be nice for a spinoff.
>I like their games' different conceptual art, and how they adapt to them.
Blizzard
>They made Diablo, Starcraft and Warcraft series.
>I believe in their capacity of writing a really good plot for Pokemon. Graphics and Cinematics would be so good I think they would do a better job even than Sq-Enix with Pokemon.
>Multiplayer experience would be boosted a lot, but monthly subscriptions would be required to play Multiplayer. DRM is also a possible option.
Retro Studios and Intelligent Systems would be good bets, but I don't know much about them.