What is the "Dictionary" pane on the right for? Anyway, nice effects, I like the way the ball leaves a clean trail and the paddle bounces when the ball hits it.

Very nice, especially the effects when knocking down balls. The only problem is that it often seems to freeze and use 100% CPU, and you can't play any more. By the way, the ball graphics are from a popular Linux game called Frozen Bubble. Does this mean you are also Linux user?

In level 2 (in Easy mode), destroying the second shield generator always kills the commander, no matter how many units I try to pack around it.

My strategy was to send all but the commander in a big clump into the middle of groups of enemies, and that way they were all gone way before the end of the mission.

What I would do is calculate the X value for each column of pixels and color the appropriate pixel. If the X difference between the last pixel and the current one is > 1, you have to connect them with a line so that there isn't a gap in the graph.