One option is to remove PDCs entirely, although that causes other issues with planetary bombardment vs ground forces.
My issue with this is that I like the idea of planetary bunkers or military bases.
Second option is just to remove hangars from PDCs.
I like this one better. Alternatively you could make it so you can only land fighter sized designs in planetary hangars.
Honestly, PDCs need a bit of work.
1) Hangar; Changes to hangar mechanics (either removing them or restricting what can land).
2) Shields; While the large bonuses to armor (in the form of several free layers) is great, PDCs start lagging behind ships in defence because of a lack of shields. I don't see any reason (unless technobabble)why they can't equip them.
3) Weapons; While others (Zincat) are saying just to remove weapons from PDCs, I think they need a bit of expansion. While Lasers are useless in atmosphere, I don't really see why Railguns, Gauss Cannons, or Particle Beams are locked through the same rule set as they all are kinetic weapons. And the only real way they would be viable is if you could turret them. Missiles are a part of this to as even though missiles have TN engines, they could be magnetically launched out of the atmosphere/gravity well. A small change to PDC launchers is that are a bit larger (while keeping the rof buff) to represent the extra bulk to launch them out, and make it so PDCs cant equip regular launchers to ballence it out. I assuming that the change to refuel/loading rates will also include ordinance, fixing the "unlimited" magazines when over a planet body, making a reason for PDCs to have magazines.
4) Maintenance; Remove the intended deployment time part of designing a PDC. It simplifies them a bit, and gives a reason to use them over a long deployment time ship. Possibly also make it so they require 3/4 to 1/2 the needed crew, as it would be easier to maintain/man a base than a ship. Also, have them cost more wealth (based on size/tonnage) to maintain.
5) Refiting/Decomitioning; This is the biggest drawback to PDCs currently. There is no way to change a built design to give it updated systems, or a way to scrap it to replace it with something else. While I agree that you should be able to change things that represent the general layout (barracks, engineering space, magazines), You should be able to change out external things such as sensors or weapons easily enough or update systems like fire control without a major issue.