I's been a while since I played a game of AIW so I might not remember all the game mechanics as well as I should... But I remember hardly ever unlocking mk III turrets. Even mk II unlocks are rare. The only ones that see the highest marks being unlocked in any of my games are HBC, tractor and grav turrets. By the time my defenses are starting to suffer, I have usually picked up 1 or 2 controllers already. That's on a 7/7 game. I have played and won a few 9/9 games and I might unlock a bit more turrets there, but still not a lot.
As to a possible solution, I don't have a clue I'm afraid. I wish it was more enticing to unlock higher mk turrets, but I also like the mk V controllers. I think I like the idea of limiting the controllers to 2-4 random ones per galaxy depending on size the best. Enough to make a difference but not so much that you can potentially build around it.