The main problem with that, however, is that it's already a VERY delicate balance. Adding more upgrades to the player without nerfing the previous ones could easily make the game a cakewalk, and i want the late game to be difficult. Also, can't remember if it's new in v0.9, but i've generally lowered the cash income for the player, so you probably won't have all upgrades before the last few levels. It is also at this point that you will notice that upgrades alone aren't going to save your hide. :U
Make no mistake though, i can see the problem with not having further upgrades past a certain point, and we might well NEED a third tier of upgrades later on. We're planning to make a New Game+ mode at some point, which will let you replay the game with your current upgrades against upgraded foes, but in order to keep that interesting, we'll need more upgrades. For now though, we should put the finishing touches on v0.9. :U
@Xantalos: But with a ship that already has instant response time, how'd you upgrade speed/maneuverability beyond increasing movement speed? Perhaps... Perhaps the Dash skill should be dependent on a ship upgrade as well. That could be pretty cool. I suppose it would be possible to have multiple levels of upgrades crammed into one button, but that just raises the question of how in the world to fill up the now twice as numerous upgrade spots. BUT THAT IS FOR LATER THOUGHT, for now we're pretty close to v0.9!
I'm glad and thankful that you guys offer so much input though, you've given us a load of great ideas to work with. In particular have i begun thinking on how to expand the upgrade system now. c: