Well, its no secret that I like the space combat system, even if I've had few large scale and long winded hectic battles, it seems to me to represent what we see in the films and the tv-show(s) pretty well, even a lot of the stuff we read in the novels and comics.
Now, I've made a simplifying decision when it comes to the initiative, not sure whether it breaks with or corresponds with RAW in any way, but I've decided that each ship, or minion squad/group, acts on one initiative count.
For the players this means that they act as they want, but have to act together, the initiative count is for the ship, based upon pilot, co-pilot or sensor operator checks (depending on how it starts), a gunner already in a turret could also decide the group's initiative I guess... any way, so whether the gunner shoots before or after the pilot executes Gain the Advantage is up to the group to decide upon. This can probably mess with some other things (like the Field Commander talent series), but so far it has worked perfectly well for my planned encounters, even though they always escape.
It gives the crew some freedom, but it is also easier to apply pressure to the group as a whole, as they all become more engaged, in my experience, than when "waiting their turn" in the initiative order. They also have to cooperate differently, and make decisions in a different manner, but also that much clearer as to in which order they go. It has been messy a few times, but I find it less messy than to let the crew's initiative be spread all over the round, perhaps less "realistic", but makes for better, or easier, story telling for high-octane chases and short battles.
This simplification does give the GM a responsibility of not ganging up and piling damage upon the players' ship like a MMO-playing moron, but rather think narrative, story and fun - not giving in to rational choice, game theory and utilitarian despotism. Remember that social contract Jay Little mentions in interviews? He didn't invent it, Grotius sort of did (and was helped along by Hobbes, Pufendorf, Locke, Rousseau and Kant up throughout the centuries), any way, this isn't Risk or Monopoly those are crap games, we all know it... - that social contract, more Little's version than Grotius' perhaps , is imperative for this game I think (any game really, but that's another matter), and moves perhaps even more to centre stage during space combat, particularly using a simplified initiative count that can easily be exploited by the GM when s/he controls many minion groups and other opponents.