The main reasons to go with 3d over 2d in an isometric setting is the number of frames for characters, and objects that need to show multiple views, and a non-tiled setting where rounding can be an issue.(Ogre Battle vs Diablo as example differences). These things can be done in 2d with great effort, but 3d makes it trivial.
With the given information the 2d isometric setting could be implemented in C3 fairly easy.
Of course the key is knowing how to do it.
The only foreseeable issue might be garbage collection.