This comes down to the old argument: Use what works for your given situation. In the case of a 2D point & click adventure(with or without 3D objects), it's much easier to use something like WME as opposed to 3DGS. You get the benefit of editors and a scripting language that were created for the task of making this style of game. Also, when using the 3D option in WME, you're walking around in a real 3D environment with multiple cameras and lights, so you aren't getting any advantages with 3DGS.

3D on 2D can be accomplished in 3DGS, but there's a ton of extra setup involved. The most difficult part is placing the sprite masks(the areas that things can walk behind) in the proper place so that the scale matches up with the original background plate. Also, you're going to need more than baked textures to pull off the detail in realtime. You simply aren't going to be able to achieve that amount of geometric detail and keep the framerate high enough to satisify the overwhelming majority of your target audience.

While the tech demo, in my first post, could be done with baked textures and in realtime, do you really think you can pull off the subtlety and detail of this Syberia II painting(click link) without the benefit of a ton of geometry? .

http://www.geocities.com/hainesrs/syb.jpg