I recently started playing Sea of Stars and what amazed me was the seamless blend of Isometric and Top Down 2D. Sometimes even in the same map. It's what I have in mind for the game I'm currently planning, but I'm racking my brain at how to achieve similar things.
At first I assumed it's a top down 2d tile map with isometric art, but then there's the added elevation that makes me completely uncertain how they achieved such things.