Wow, great concept! It's true that the physics are a bit screwy, and the game gets a bit repetitive, and the game seems to suck up system ressources like a sponge... but those things can be remedied! I'm confident that this concept can evolve into a fabulous game.
As a suggestion, you might want to have at least some levels (if not all) that focus on time rather than clicks as the score variable - it's just more fun to play for speed, since you get to click more and control the ball more. How about several balls at a time? Even co-operatively? Check out the Sola Rola flash game for inspiration on that.
Hmm, it would be nice if the edge of the screen wasn't also the edge of the playing field... when a villager lands close to the edge, it's actually quite difficult to pick him up, simply because he's partly obscured by the "edge" of the game. This could be remedied if there was a small area on either side which the villagers have to get to, like a "safe zone".
Without a doubt, this game is among the top five on Kongregate. Fantastic level design, unique aesthetics (for a flash game), and just generally solid gameplay.
A few more things:
Autofire really would be nice, maybe a Boxhead-like solution where it's unlocked later in the game... I'm guessing a 10 minute game can rack up over 1000 clicks...
Also, the soundeffect for powerup pickups has a tendency to produce audio clipping, especially when there are a lot of them. Something as simple as lowering the volume should fix that problem. I think this is extra important because this is one of the few flash games AT ALL that has reasonably well mixed and leveled sound.
First off, the (presumable) inspiration for this game is nearly rip-off. It's basically flOw with guns.
Moving right along those lines, this can't really be considered a "game", since there is no winner or loser. That's not a critique, but I do think that a scoring system (at the very least) or a challenge mode would suit the competitive nature of Kongregate much better.
As for the design, my critique is mostly cosmetic. With such simple design, it gets confusing with the bubbles. The small enemies look like powerups, and the enemies shots look exactly like your own... a few color changes should fix that, and you don't even have to create a single new graphic.
I have to add to DingoEatingFuzz's little outburst that... it really, really does not register all clicks. I would wager that it's because the refresh rate of the flash file is lower than the refresh rate of the mouse, so it only checks for clicks on every frame. Either that, or there is a layer getting in the way, like the stars for instance... I don't think that's the case though.
Please get over your narrowmindedness and consider these six pages of free usability testing.
Well, fun idea, but very very difficult to play, mostly because of the start-over rule when you hit something.
Also, some boxes on the edges are impossible to circle, not to mention that there is no margin, so often the mouse coursor will simply leave the playing field, and not have any effect on the boxes.
To put it bluntly, this game is too easy. MUCH too easy. After playing for about 2½ hours I still hadn't taken any damage, and had around 500.000 xp that I didn't know what to do with. Even with just standing around and not firing, it took several minutes to die. This type of flash game is NOT the kind of game that you will usually spend many hours playing.
Higher difficulty, and more variation. Levels with different objectives would be nice for instance, or a way to improve highscores without having to play for hours and hours (such as combos / rapid killing for instance).
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