soulfulness has nothing to do with 2D or 3D, but more to do with mass market commercialization of games, where the creative vision is not from an individual artist (or very small number of them), but via design by committee, and various managerial interference for profitability and market appeal.

That's why you will find the modern AAA games (which is of course 3D) very soulless. However, the same soul still remains in indie games.