Cloud and Tifa will be the main character or should it be Aerith
-Materia has been replaced with Pokeball -Sephiroth is Champion and the Evil Team Leader -Aerith will not die since its a Pokemon games -Yuffie steal some of your Pokeballs -Professor Hojo will be your new Pokemon Professor
No seriously, I'm gonna have to say AlphaDream, the folks in charge of the Mario & Luigi RPG series. They have a great handle on graphical styles (though Dream Team could look better), know their way around a battle system and a great script and they have a working relationship with Yoko Shimomura for music. Think of the gloriousness of a Pokémon soundtrack composed by her.
I would prefer to be known as BlackWaltzTheThird, or just Waltz for short. Got Animal Crossing? Join today! http://www.esoevil.com/forums/index.php
Atlus. Not only could they up the challenge, make better storylines and lore, and maybe even up the maturity in a spinoff or two if not the main games, but it also opens up the possibility for a Pokemon x SMT game.
Not to say they'd do it better. Gamefreak has done the formula well and I doubt anyone could surpass them in doing it how they have been, but Atlus would add a breath of fresh air to some things.
http://25.media.tumblr.com/tumblr_m6nh9mNfm11rnkfgmo1_500.jpg Gen 5 FemAce is mai waifu.