Ask yourself what going 3D will add to the game.
Negatives to 3D are that it is harder to visualize, and represents a vastly more complex world to work with.
Positives are that it represents a vastly more complex world to work with. (You have to pick if that is actually a positive or negative impact on your game.)
Personally I like 3D when it comes to something that I explore, but control relatively few things in. 3D strategy games become far more complex and aren't always actually an improvement over similar designs done in 2D fields.