I appreciate the constructive criticism! Were you using the starting laser all the way? I intended for each subsequent weapon to be stronger than the last after getting enough upgrades into it, but I've had people who didn't feel incentivized to try the new weapons before, which leads me to conclude that the weapons need a rework. I'll probably end up moving away from being able to upgrade every single weapon stat altogether, since as you said, it might be nigh impossible to balance.
Good point about having the tractor beam be able to penetrate the walls from the get-go, having those crystals slip away is frustrating. There's an upgrade in the late game that makes pickup-eligible crystals become unable to pass through walls, but I'll probably keep as an upgrade, since otherwise collection would become a bit too easy.
My furthest plans involve giving the player a choice between asteroid-rich and enemy-rich levels as he progresses, so I hope the game will suffer less from doing both at the same time.