Classic, classy, and ... good
This is seriously one of the best games on Newgrounds I've played, except for one thing: it's too shallow. I had a couple ideas that you may or may not care about for (if you even decide to make it) the sequel.
One main problem is that, even though the upgrade system is really cool, it's way too linear. It would be awesome if there was a system to choose between adding shielding, offense, speed, etc at the expense of bubbles. For example, when my tri-cannon was replaced with the super cannon + normal cannon, I found myself actually weaker to an extent. The tri-cannon nets you more bubbles AND the bullets are faster. If you could choose between the two (or maybe even others) that would really improve replayability.
Another thing is, like somebody else suggested, bosses. Random cells should have a boss, ex. a giant thing that spawns other enemies. A minimap that shows which cells have been cleared and what cell you're in (just a basic X/Y coordinate) and a save feature (simply saves your current cell and the cleared status of every cell in a text file or whatever, as well as how many bubbles you have) would also REALLY improve the game.
Even without all these things, the game already deserves a 4/5. And believe me, I'm not one of those people who just fives everything like an ass-kisser; I genuinely enjoyed the game. Spent about an hour playing it.