It's a tough call: full 3D or hybrid 2D/3D or full 2D. I understand the decision you're grappling with, EDI, I'm tossing the same thing around in my head right now.
Part of me is very tempted to do it pure 2D, but I like the idea of a 3D terrain and some other 3D effects (particle effects, lighting). These obviously have the advantage of being a bit easier for those without artists (like myself).
Of course, given a talented 3D modeller, I'd go with pure 3D as it would dramatically increase the amount/quality of the animation (see Silent Storm for an excellent example of a pure 3D "isometric" engine).
Considering that Photoshop is my only art tool (that I have any skill using), I'll be doing a hybrid approach. Characters will likely be 100% sprites/2D, with environments being 3D (buildings, terrain, walls).