However, when I'm developing a game, I can tell you that it's much easier to find tools and libraries for developing 3d games than it is to find tools for developing isometric games these days.
relevant to that point is that with the power of cpus and 3d modeling tools.. it seems to me that it's become easier to actually use a 3d engine and 3d models, but simply restrict the game to a fixed pseudo 2d / isometric view.
that is, in the old days it was easier to hand draw images for a 2d game.. but it's gotten to the point where it's simply easier to use all 3d models and engine, but simply fix the camera angle to present an isometric or 2d view of the world.
one of the few but serious problems with this approach is the collision detection stuff, which is so clean in 2d but doesnt transfer over to 3d models and 3d engines.