Hola, interesting to listen to this here. Now, once again I state, this game will be 2D for at least the first full working version. Maybe by the time I finish, I'd be a good enough programmer to consider branching into 3D, but the first version will be 2D for sure. Here's my quick 'neutral' comparision of the two formats:
2D
Pros: Easier to create, graphics designers more abundant, classical style (never did FFIV any bad), engine simplicities, cellmaps work well, sprites are easier to use than particle systems, less memory needed, easier to create cutscenes
Cons: Cutscenes can't show as much detail, such as emotion (are you crying there?), can be harder to express story, that hot girl won't look so hot as a sprite, perspective woes?
3D
Pros: More detail, cutscenes show a lot more emotion etc, increasingly common (oldtimer classical gamers are dwindling), multiple camera angles, 'better' graphics
Cons: COLLISION!!! (so many games have problems here), larger file size, cutscenes take 100x longer to make, skeletal rigging, game engine complexity, particle systems (vs simpler sprites), modelling takes a lot more work, complexity (!!!)
@sand, RPG Maker is no longer being used. Still open to engine suggestions. One I have found (untested), is Allegro, which is meant for 2D and may be good. Another alternative is to use a 3D engine with GOOD 2D capibilites (all 3D engines have at least some degree of 2D, but not always good enough), then we can have adaptions in the future (distant, distant future) or even add some degree of 3D elements to a 2D game.