To elaborate on the bug... it appears that some of your puzzles don't have one unique solution. You're probably determining a win by matching the pixel pattern, but you should instead be determining a win by checking that the row and column requirements are all satisfied.
Is there some kind of bug with the ranking stars. I've gotten everything through gold for the main story missions, but I can't even get bronze on most of the others. What do you have to do?
The enemy movements are just TOO random, which turns it into a game of chance and waiting. If they followed even a rough movement pattern, it would be much more interesting.
I keep having a lag problem. It starts fine but progressively gets slower. I have to navigate away from the page and then back to get it to speed up again. Anyone else see this?
I don't think the game is very well balanced with regard to the colored pixels it sends you. If you're unlucky enough to not get lots of orange pixels and max out the gun speed by around level 19, the game is literally impossible. You just can't fire fast enough to hit even a fraction of the targets! Send more orange!
I liked the first one, and I like the addition of dimension switching now, but there are WAAAAY too many colors/abilities now, and having to use the keyboard for all of them is just too clunky.
My suggestions: fewer colors (maybe 6 max). Also, the gauges on the side to show color power are good, but you should change the color of the center of the pod to the "active" color. This is the color currently selected, and it can be activated by a keypress (like "enter"). The active color can be displayed on the pod as a muted color when that ability is not yet available, and an intense color when it can be activated. These colors can then be scrolled through with the mouse wheel. I think this would be easier than using the keyboard so much.