I'm not sure what you mean with "3D" here:
-you can do "true" 3D and lock the action to the x-y plane and the view to overhead. I would not recommend this for a first attempt.

-you can do 2D (i.e. sprites) via OpenGL. This is what Arc does. If you want do it yourself you'll need to learn some basic OpenGL commands. This can serve as good introduction to OpenGL if you really want to go 3D later on.

-you can use images of prerendered 3d-models as your sprites, depending on wether you find it easier to learn how to draw or how to model and texture.

>>If I were to do 3D stuff, would Blender be a good choice for a 3D application

Blender is fine, though personally I prefer Wings (http://wings3d.com/) for modeling.