Phthisis: I've come to like thy group's idea more and more (looking over my shoulder for Sigoroth... sorry Sigoroth!). I have an interesting idea for expanding it I've partially borrowed from another group who re-worked the main Warhammer 40K: strategy points. Essentially, this is a way to incorporate the limited information and command and control facilities available in battle that the original BFG chain of command and random leadership was designed to replicate.
Essentially, a fleet has a pool of strategy/tactical points that they get from the size of the battle or via fleet commanders. To use Special Orders, they remove a strategy point from the pool and the Special Order is passed automatically. (In the WH40K version, I like the idea of every action taking a number of strategy points but in BFG I think this more limited version is better). Also, fleets need a certain number of strategy points to disengage in one go; if a fleet uses up their last points in a desperate gamble to win the game, they can now only disengage individually, allowing the enemy to exercise their wrath as they disengage piecemeal. Finally, strategy points can be expended in deployment so that one's fleet can obtain a more advantageous position at the outset of the game.
A player now has choices in list composition ("Should I take more Fleet Command and get more special orders or should I take more actual ships to cause damage?" - representing the trade off between tactical assets), during deployment ("If I put my ships here I'll have less special orders but I will begin the game outmanoeuvring my enemy...") and during the game, since the strategy points are limited in availability. Choosing not to (or not being able to) spend strategy points represents the command and control elements of the fleet being unable to cope with the battlefield circumstances and the lack of information.
Leadership is no longer really required though, so it would need other things to represent (maybe more strategy points for squadrons with higher leadership, attack craft interactions, navigation etc.?) - I think that having a crew characteristic is good though.
I also like the other things thy group uses to make the fleet more interesting! This is essentially my original idea, that fleet commanders can take some 'Traits' that give the fleet or their squadron (for secondary characters) characteristics; something like AndrewChristlieb's suggestions but able to affect the whole fleet. E.g a fleet commander takes the 'Long Deployment' trait (a disadvantage analogous to the ones in the main rulebook's campaign section) but is now allowed to take the 'Expert Crew' or 'Extensive Scout Knowledge' traits which provide bonuses for crew stuff and strategic points respectively. Perhaps this tree idea is best?
Horizon: I have seen some of Sigoroth's ideas but it was a while ago... I liked many of them, though.
Fracas: What do you think of my alternative suggestion? Perhaps fleet/squadron traits can represent random leadership better (e.g. a fleet just out from the Academy will have no battle experience but fresh ships and crews whereas a fleet/squadron that has been engaged near the Eye of Terror for a while will have damaged ships and crews but experienced and hardened crews).
Thinking Stone.