Really very good.
Just a few suggestions.
1. Add an indicator to the mini-map showing where your ship is, even if its just a blue arrow or something showing which sector you're in.
2. More weapons, plus the ability to switch between different weapons, maybe even add enemies that are susceptible to certain weapons and resistant to others.
3. More maps and more enemies, 40 waves on one map with only different types of enemies made it a little repetitive.
4. Add the ability to sell/replace turrets, i'm sure your idea was to force people to choose whether to simply buy turrets or save for the missile launchers, but it was almost a no-brainer to buy basic turrets, since it took f'ing ages to save up the amount of cash required to buy more than maybe two rocket luancher turrets.
5. Perhaps add different ships? Something we can select at the start?
6. Allow us to fly over our base, perhaps even allow us to replenish our shields by flying over the core, in exchange you could reduce the amount of shielding we start with or increase the damage enemies inflict.
7. Perhaps add purchasable allies that fly around shooting enemies, either alongside us as wingmen, or on their own as guards.
8. Additional game modes, an inverse game could be cool, have the base start fully upgraded with guards, then have the 40 waves as usual, but this time you're one of the attackers, the base would repair between each round, and the guards would heal and be replaced, each wave of attackers would get stronger as usual, the game ends when the core dies, and you gain points for doing it in as few waves as possible.