I think the real fix for Queens is to limit how many you can take in a fleet, and to completely remove Flight Computers as a SHIP trait, and make it a Queen-centric trait instead.
Queens should be limited to what priority you buy, so if you spend 1 battle point on a Queenship, then you can -ONLY- have, in ADDITION to that Battle-level Queen ship, two Raid-level Queenships, and four Skirmish-level Queenships.
This has two focuses and effects:
1) It encourages people to buy the highest level, most protected Queenship on their list to protect their Queens and open up the number of Queenships they can get.
2) It actually enables the dynamic that Gaim have where if they lose all the Queens they suffer dramatic penalties.
As it stands now, you might as well remove the rule where if there are no Queens you lose all the bonuses as people hardly ever take anything but Queenships.