First let's clear some things up. I suggested a 3D enviroment simply for ease of use in positioning characters, behind and in front of items, secondly so you could use a 3d coordinate system for where to place objects.
Secondly to have camera movement inside a 3d room, I still don't need 3d character models, they can still be scaled sprites that are always facing the camera, think of the old sprite/billboarding technique used in wolfenstein 3d, and Doom...
Thirdly if you have any kind of horizontal scrolling it would simply look neat if the enviroment changed perspective as you were moving, in most cases a 2d sprite character would be mainly in the center of the screen, where the background is moving behind him, thus you don't need a full 3d model for that.
Finally I'm not saying not to have 3d characters in there if you want it... I'm just saying I still prefer 2d, but there are some things in 3D that might be a bit better even if i'm just using it to do 2D...
If you notice some of the latter disney cartoons, they use 3d for certain things to some extent, while still retaining the 2d cartoon quality of traditional animation.
For instance way back during Alladin, when escaping the Cave of Wonders, the "lava" portion of it was a 3d mesh that was textured with a hand painted lava texture.
Currently in Treasure planet, they actually did 3d models of the ships which were textured (I think with hand painted textures), where they still did traditional 2d cel-based animation and matched-moved the animation elements with the camera, so the animation would be in perspective.
Now if you're thinking i'm talking from a purely developer standpoint, consider how you have to create objects that can be walked around in the editor, you have to create the way points, and you have to have a sprite element overtop the background to get the player to walk in front of or behind and object. You also have to set the scaling attributes for a room, since it's purely 2d.
If you did this in a 3d room, you would simply place elements through a modeller style editor (although i'm not talking about modelling the enviroment in wme, but just for placement of objects). Set your z position and your x and y ( or just x and z ), and the engine automatically scales the sprites appropriately based on the distance from the camera.
Now, this all sounds complex, and it probably is, if Mnemonic can't do something like that I totally understand however, I think that there's greater flexibility when adding 3d elements to basic 2d scenes...
Plus, if he did include both 3d models for characters, and/or 2d sprites for characters, you could conceivably create characters or objects that were half hand-drawn, half computer generated. (See Treasure planet also for this, when they attached a mechanical arm to Long John Silver, which was modeled in 3d and attached to the 2d animations of Silver)...
All in all you could still achieve a hand drawn look, and still do hand drawn stuff for sprites, and hand painted textures to look like a cartoon, but with a greater flexibility and power than wme currently has.