While I enjoy the concept - it certainly is something novel - there are a couple of things you should factor in, if you're thinking about improving it.
Another user stated the game lagged badly; since I'm not a flash expert this may not be your fault but maybe worth looking into, if it occurs to other users, as well.
As for the gameplay:
Start out with levels that have a simpler layout. For example an introductory level with only 2 rows of balls instead of five. Reduce colour variety, as well, in the beginning, so as to give the player time to familiarise themselves with the game mechanics.
People are inclined to skip the intro, if it appears to be lenghty, so why not serve them the How To Play packaged in the first few levels, where they can learn the game mechanics intuitively, instead of overwhelming them with having to take on the full game instantly.
The lay out seems too crowded for a beginner to instantly grasp.
-You don't need two Score displays (although I applaud the Score being featured in the center of game play action - makes it easier to concentrate on the game while aiming for High Scores).
-There is too much text constantly on screen, which distracts players. Score/Highscore and Level numbers don't necessarily need to be tagged with text, and hints or explanations shouldn't be on screen for an extended period of time (not sure whether that was intentional or not).
My suggestions are as follows:
-Move Sound/SFX/Back to Menu /and/ General Help options in a collapsible menu at the bottom where they don't distract players (red and white outlined text may be easily legible but also constantly begs for attention from the player).
-Move the explanatory symbols (the written labels are helpful because you made them hover-accessible) also to the bottom, maybe to the left, where Sound/SFX are right now. While playing, a user will want a clear look at what's important: Scores, Targets and Remaining Balls.
-Remove the double Score and labels for both Score/Highscore. Space out the inner circle so you can squeeze the Highscore under the already existing Score, and remove written labels for both. Players will quickly know, what they're looking at.
-Keep Target and Remaining Balls at the top left, so players can easily check how they're doing during a level; written labels are strongly recommended here.
[You could also move the Level number to another corner, and remove the written label, since it isn't imminently important during gameplay, but that's trivial.]
You kept the game style itself rather simple, which I find pleasing, although I would have chosen different colours (the neon green and yellow may be hard to discern for some players/on certain screens).
The 3D animations a slightly wooden, however, I don't have any experience with flash/animation, so I have no measure of reference whether you've done a good job or not on that. Still, I liked the floating feel you tried giving by the slightly moving back bases (?), and supposably intended to be fluid ball movement.
The theme is catchy but non-obtrusive, I've had it toggled on while writing this review, and I haven't yet grown weary of it.
To me personally, the sound of the balls clicking against each other is entirely orgasmic; I fucking dig that.
The harp sounds are also pleasant, despite not really fitting with either the theme tune or the general theme of the game.
Clearly, you've put a lot of thought into this, and possibly thrice the amount of frustrating at times work hours, which is why it'd be sad if your game went unplayed for the most part.
The only thing I can say about this game is: WTF???
This was not (in my opinion) a good game. it lags badly, there is no real point to it.