Pretty fun game. I finished it.
The sense of power was fun. The ability to switch ships was good too.
If you make another game, you should focus on several things. Give upgrades (faster regen, shield, faster fire) and special abilities (cloak, mega blast, heal) you get from bosses.
Make some slightly more in depth storyline. Maybe have a few factions- religious, cyborgs, rebels- have them give you certain goals during missions, like possess a certain number of ships, destroy certain structures, in return for money for upgrades. Have a twist at the end, like it turning out that the government forces pursuing you are controlled by your prototype, or plugging into the global ethernet and finding you are not the first AI to escape.
Or even, alternate endings for each faction, with a special mission at the end for each- for religious, being put into a human body as their messiah (crystal dragon jesus!), for cyborgs, put into a robot body as their king, for rebels, taking control of the government's mainframes. Maybe with some sort of morality metre.
Finally, a few more sorts of enemy ships. Ones that can force you out of a ship. An energy recharge ship. One that slows you down after you leave it. Ones that lock you in until they die. And, maybe give us some chance to control bosses mega ships for a bit, since that looks fun, maybe with a bonus level involving that.
Thanks for a good game.