I've got some ideas on how to adjust the Gaim fleet organization.
Assault Drones - rolling two dice seems a bit over the top, but boarding actions aren't that common, so it's probably OK to keep this rule.
Pilot Drones - it should take some type of training to get the pilots ready though. and even if you get the pilots for free, the material and parts to build a fighter has to come from somewhaere. Suggest 1/2 cost rather than free.
The Queens. - broken. There's virtually no incentive to take a fleet that anything but queen ships in it. It gives them the same ability as Vree (even with one queen onthe board, it is the nearest queen) and no real basis for it. Suggest only ships activly squadroned with a Queen ship recieve the +1 CQ bonus. Also, there are too many opportunities to bring Queen ships due to the varied PL of queen ships (which are a required component of the force). Suggest modifying this rule so that while a queen ship must be taken, you may not bring a queen ship of a lower PL than the game being played. IE, you can't take a skirmish queen if you are playing a raid-PL scenario. You can't take a raid queen in a battle scenario. This would require making more queen ships for War and Armageddon PL games I believe, which isn't a bad thing right really. more models! As a stopgap, allow battle-pl queens in War an Armageddon PL games.
Dynamic squadrons - I really don't like this rule, but with the above changes it may be tolerable.
Protect the queen - this is a drawback rule, that will only matter if the number of queen ships can be limited in some manner. With the above changes it may function as intended.
Ships - crewed missiles have to fly a more direct course to collide with a ship, and so should not have such a high dodge rating. suggest lowering this to 4+, or, 5+ on the turn thay intend to collide with the enemy.
Shuuka skirmish queen ship - 40" mines are over the top for a skirmish ship. recommend combining this to a turreted 20" mine with 6 AD instead, and add some short ranged pulse cannon type weapons.
Stuteeka - reduce carrier ability to 6.
might be others, but those are my thoughts for now.
Chernobyl