It's like a 3D RPG, like the handhelds, but with all the regions rolled into one, a little like the Anime. You completely customise your character, and they begin in Pallet Town.
Did you know character customisation in 3d is hard, beyond Painting? Take PBR for example, Cool Girl has lots of Tank tops, and has no Jacket. Why?
As a 3d artist/Poser User, I can explain. Cool Girl model probably has the tank top and trousers already on her. Each design of top is "painted" on. (Why else does Soul Calibur 3 offer all those colour options with most Parts?)
Chances are they will not use "Publicly" available Human Models like Daz 3D's Victoria 4, and they Make their own. Making a model and then making conforming clothes.
If the clothes don't conform you can get "Poke though." For example, take the Cool Girl. Let's say her tank top isn't done correctly, whenever she wave her arms, her boobs pop out. Turns a child's game in to a instant ESRB AO.
This example unlikely to happen as Most games will have added on the non-moving under clothes to the base model. (This trick also is used in the Poser community.) "Poke though" happens alot around the Torso due to connection of the joints. Example of Poke though:
http://bignutter.deviantart.com/art/New-Jodi-Test-60376357
Conforming clothes also add the problem of that the Processor has to draw each extra item of clothing. (Personal Experience of using Poser-like software.)
The alternative is creating models for each outfit, or at least parts of the model, which eats more Disk space.
Disk space is quite likely a premium with RPGs, espessally with Pokémon, You've got over 500 models to start with, and that's just the Pokémon. Add the fact you're adding over 40 trainers(from RBY alone), and Several NPCs.. Then there's the Landscape in a higher defintion than any of the games.
It may just be impossible for all that with the current Disk size. Even guessing that all the Pokémon take approximately 1.5gig's you're still asking for a lot. If not in Disk and Processor power, but in Man hours to build it.
Chances it took over a day to lengthen Rui's Skirt and top.. most of was probably to make sure her skirt wasn't "Digging in" to her legs. (Rui, is the Girl that follows you around in Colosseum, who has a shorter top and skirt in the Japanese Version)
Just in case you ask how do I know this:
http://bignutter.deviantart.com/