I believe that the planetary defenses need to be rethought. I like the idea of the hangers with the mobile squadrons that can cover the entire gravity well, but the turrets are way too underpowered for what they do. Their range is severely limited, which means that a group of seige ships can fly into an area, dodge the turrets, use a couple of fighter squadrons to take out the bombers headed towards them, and then assault the planet with absolutely no trouble.
To this point, I suggest two things. Either, possibly, make the turrets missile based and change the damage output based on the range between the turret and the target... or take the turrets, shields, hangers, phase jump limiters and pretty much all the other defenses and place them on-planet.
Imagine. If something is attacking the planet and the turrets can't hit them because they're out of range, do you think that the people on the planet are just going to look up and watch themselves getting bombarded? We'd shoot every missile we had on the planet up at them in order to defend ourselves. Instead of placing defenses out in space, lower the damage output a bit and then place them on the planet itself and give them the ability to fire outwards from the planet to the yellow line dictating where the orbits stop. Ships would still be able to 'dodge' the defenses by flying on the outside of the well, but once inside of their range, they'd start to get bombarded. This would make the user decide on whether they wanted a soft target [read: Capital Ship Factory, Refinery, etc.] or whether they wanted to try to survive the attacks from the homeworld and try to take out the planet itself.
Right now, dodging defenses with the cunning use of a shift key is too simple. The only thing you ever have to worry about it is the computer's other fleets. If the planet were able to protect itself no matter what direction I attacked from, it would bring a bit more interest to combat and leave the computer with a little bit of protection in case their fleets are half way across the galaxy.
This would also help clear up issues with clutter in the gravity wells that prevent ships from flying properly from point to point.
Just my two cents!