What could be improved? I dunno...
Well, you COULD go around playing other well-made defense games, such as Orbital Decay or Flash Defense TD to see if you can add various features to your game.
I think that you can't go wrong with the addition of a player-controlled main cannon. The trouble with a main cannon, though, is having to spend the time and effort to balance the power in skill required to use it compared to being totally dependent on automated turrets.
The addition of making spaceports to send ships would be nice, but the main problem with them is that the effectiveness of sending your own units to the enemy has been shown time and time again in many different defense games. The only defense games that I've seen that effectively uses the sending of your own units against attacking forces is Orbital Decay and other games that use the units as distractions, buying your main gun time to take out the enemy. Actually, Orbital Decay does this remarkably well, making each unit have an AI control that enables them to actively dodge oncoming attacks.
On that note, the dynamics of enemy movement would be nice to have. The movement of the fighters out of the carrier units appeared to not move in a set up-down movement, but instead, in a way that made them seem like they could fly around like 360 degree top-down shooter.
Adding other elements, like the Rock-Paper-Scissors type element system in games like Flash Element TD can be a double-edged sword, bringing extra diversity of gameplay while at the same time making things more complicated and frustrating than necessary for the player. The only frustrations that should be given to players are those that the players choose for themselves: in other words, difficulty levels.
I, personally, would definitely like a defense game with gameplay options. Maybe that's why Generic Defense Game became so successful. Perhaps a Generic Space Defense Game would work, putting in elements of top-down space ship shooters, tower defense, and tactical defense.
As for this particular game, Apocalypse difficulty was definitely difficult. It forced me to change tactics in order to finish it. The Apocalypse endboss was totally awesome, and certainly surprised and challenged me.