I agree 100%, I find isometric games to feel and look much nicer than 3d games.
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.
And that's another thing which may be a determining factor, especially if you're a lone developer pressed on time.
I have yet to find a decent Free isometric or even high-level 2D game SDK for C++, but there's plenty of them for 3D games.