Yeah, the controls definitely take some getting used to. I think using the mouse wheel is easier than the arrow keys (especially if you have a free-rotating mouse wheel), but being able to move or rotate the square by moving the mouse would also be nice.
I agree the side graphics probably aren't all distinct enough...even I was getting them mixed up sometimes when playing!
When I was testing it, I liked having a little bit of a breather in between waves. I did make it so if there are no balls left on the screen, it'll move up the spawn time of the next wave, so there shouldn't be more than a couple seconds of downtime. I never tried just having constant spawning modulated by the number of balls remaining though, which might work better.
Thanks for the feedback!