The 3D environment is unnecessary but very cool and that's a big thing that I like in video games. I only wish that it were larger somehow, with more to discover over time. And maybe the "prestige" concept can be dressed up as taking the ship to different places.
As for the core gameplay, the upgrades felt a bit linear. There isn't that much choice at any given point and often some of the options available are clearly much worse than others. Also, I really don't like when a game makes me mash a mouse button. I would much prefer some minigame for energy recharging, or even just turning a wheel (hold click and move mouse in small circles) or something.