Odyssey could use another shipsystem, Plasma burn may be nice in Player hands, but it's a press to suicide button for the AI, Maneuvering Jets, Phase Skimmer or Phase Teleporter would perform better in AI hands. Also a buildin surveying equipment would fit the Odyssey.
Broadside Ships AI should be fixed in Combination with frontshield hullmod.
14Legion could get it's large turret changed to composite.
Missile Autoforge could regain a charge by consuming a destroyed ship.
Selling blueprints to official markets could allow this faction to use said blueprint.
Conquest could use a slightly larger shield arc.
Idea for a new fleet size limit:
Military ships cost 2,3,5,8 fleetpoints by size civilian 1,2,3,5, you have ~150 fleetpoints to spend (numbers are based on the fibonacci series, which is often a very good fit for balancing),
this way you could use e.g. 30 military cruisers or 75 military frigates or 18 battleships, if speed reduction in nebulas would be based on average speed of the fleet this would make small ships way more interesting.
Respecing officers for storypoints in both skills and personality would be nice, you often find good offices with personality not matching skills (e.g. rekless + carrier skills).
A tactic screen allowing to define rules for the AI when to do what would be nice: (Dragon Age Origins is a nice example)
1 Enemy Overloaded -> Fire Harpoons
2 Enemy combinedflux > 90% -> Fire Tachion Lances
3 hard flux < 25% -> close in
4 hard flux > 75% -> goto 7
5 combinded flux > 75% -> activate fortess shields
6 allied flux > 75% -> shield it
7 hard flux > 75% -> retreat form frontline
Officer lvl could increases the max length of the ships tactics.
Offset Pather interest by -LP Reputation.
Additional Commission effects: Tri Tach friendly Remnants Hege Licenced AI Use (no checking expedition AI doesn't dare to go rouge) LC lower Pather interest ...
Factions that don't offer commissions shouldn't sat bomb on territory conflicts.
Autofire should respect alternating fire settings.
Dispatch hardflux at 10% rate with active shields could be changed to convert hardflux at 10% dissipation rate to make it more useful when still firing weapons.
Time between deterioration and decivilization should be increased.
Armed Timer for Sabots to make them less useful as a dagger.