One: There's an annoying glitch. If you get all the upgrades before completing all the levels (I quit level 16 a few times right before beating it to make more money) then it goes straight to the boss and you can never get the "level upgrades" you missed. Hence my odd pattern of achievements.
Next, the review. I still think the concept of this series is brilliant and this time around you did so many new things with it, creating something with a quality I don't see much in flash games: whimsy. After upgrades as always the visual effects are gorgeous as are the sound. Now, the criticism. The game is funny enough on its own (I mean, that low groaning noise is hilarious) that you don't need to resort to self-parody of flash games in general. I thought the indie thing was cute, but I found the sheep thing vexatious and the BGM upgrade gave me an unwelcome flashback to the sixth grade. I do prefer the last game for several reasons. One, I loved the way the graphics spoofed videogame history- with the first being atari, the second being vector. Two, and most significantly, the ship upgrade mechanic was significantly superior. In the first game you could layer parts on top of eachother, allowing for far more creativity. Using parts in unconventional ways you could still make something that looked like a unique and distinct "ship". This grid mechanic is a step backwards. Your ship no longer looks like a ship but rather some sort of bizarre fleet of ships and assorted space debris, which later in the game resembles a awkwardly wriggling square. There are things about it that I like, namely that unlike the previous game you don't have to constantly reposition parts to achieve perfect symmetricality, and that when you click on parts to upgrade them you don't move them, thus necessitating more repositioning. I hope the next game you make combines the ease of the grid mechanic with the aesthetics and freedom of the original mechanic.
All in all a great game, I only mentioned the flaws because I think it would be even more magnificent if its potential were totally fulfilled. Keep up the good work!