this is a nice idea, mixing strategy into an otherwise arcade-style game. I like the waypoint system but I think it needs to be explained better in the tutorial and highlighted with visual cues when you set the waypoints. Once I did figure out how to use it, it felt nice flanking the enemy or distracting the circle of laser ships so we can pick them off one by one. The overheating mechanic adds good anti-spam but I do think it can be balanced better with enemy health and weapon damage. I also didn't feel like thinking so I just bought the standard ship every single level and it worked out most of the time hahah, so overall balancing is in order. The sound effects are cool, so are the ships. I did notice my game would lag severely when I had like 34 ships shooting a shit ton of bullets, but that's probably related to me playing in browser mode.
I didn't beat the giant at the end unfortunately but I did have fun playing. I think if you improve the movement (imo moving and shooting in the same direction does not leave room for skillful play) and balance, and also polish command mode, you'd have a really nice game in your hands. You're on the right path.
Keep up the good work!