Upgrades should always improve the ship! (Burst is a bit broken)

Draikan, I do see what you mean and although I haven't done the math on paper, I've thought about the dps before I make upgrades before. Your point as well as Lurkily's points have made me understand your side better. That being said, it's just a matter of re-balancing the benefits and penalties of the upgrades. But I still think we should have some penalties, because it creates specialized weapons. Like you said, dps should never decrease (unless the benefits of the upgrade adequately outweigh the loss), but upgrades should still require strategy and thought. I shouldn't just be able to fully upgrade my projectile cannon and have the best projectile cannon in the game, because then you're turning this great game into a twist on tower defense games. Perhaps each weapon should have two upgrade paths that the player can find through trial and error (long vs. short range or fast vs. slow fire rate), still leaving the player with strategic choices to make early on in the game.