Focus on stunners and armor-melters, all in a clump (that way the stuns are taken advantage of), and then when the boss mob has passed your gems, pull them out and bomb him with them.
Awesome game, thoroughly enjoy it. The graphics are awesome, the music and sound effects are excellent. The gameplay was very satisfying. Already looking forward to a larger, more complex sequel.
A tally of "total dollars earned," "total population grown and/or lost," and tallies of various numbers / sizes of ships destroyed would make for a nice addition in a sequel.
It would be nice to be able to direct weapons to focus on capital ships or non-cap ships.
Much of the strat for beating hard (for me at least) early on involved "juggling" aggro between cannons. I'm not a big fan of this kind of required strat... but that's just me.