Good game, everyone else has said why. I particularly like the way your base is actually a moving battle station, actually blasting it's way through your enemies, rather than waiting for them to come to it.
One star off because of the excessive grinding required to finish the game (which no, I haven't done yet).
A few suggestions to improve gameplay:
1. have keyboard shortcuts (1,2,3, etc.) for your special skills. Rather than only having the skills appear when you click on the screen, the skill bar should always be visible in the corner somewhere so you can see which skills are ready or still cooling down. Also, why limit to 5 or so skills on the bar at a time? At least let the player buy more slots.
2. You shouldn't need a special skill to aim your weapons. For example, press spacebar could activate aim mode, where all your weapons aim at your mouse cursor. Spacebar again to return to regular mode. Or gemcraft style, where you click on an enemy and all your weapons target it.
3. An easier way to re-arrange your weapons. Allow you to move stuff around when the game is paused? Allow for saved weapons layouts, which you can select from mid-game?