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Large scale world.
+ 151 pokemon to be modeled. EVEN MORE if we're going beyond Red/Blue
+ different animations for each pokemon
+ putting in several different trainers AND animating them.
Also don't forget items, coming up with a plot, maybe bosses/gym leaders.
Visual Effects for moves. Possibly voices.
3D cutscenes that'll probably be seperately animated.
Oh and Customizing your Player Character? Forget that shit!
Ever wonder why the 3-D pokemon games don't have all the pokemon? Or if they do, it's that shitty Colosseum play? THAT'S your reason right there. Just the sheer amount of WORK they have to do to get something like that off the ground.
I'd say, the best thing to do is to take your 3D game. Count the number of enemies, number of bosses, number of Playable Characters, number of NPC's. Compare that to pokemon.
Nuff said.