Since someone already started a house rule thread, I figured I'd add on rather than create a new one. There are several things about the game I can't get around (the activation order, the fact that the Init roll lets you choose who moves first and who shoots first, the fact that smaller swarms are favored, the fact that Init sinks become almost mandatory for some fleets) plus a few smaller things (stealth and interceptors being two).
So here's the house rules. These are rather major changes, by design. (my comments in parenthesis):
1) Fleet Limit: Fleet limit: a fleet commander can only control as many activations as the commander's ship quality + 6. (assuming avg ship quality is 4). The fleet commander is assumed to be on ship with the PL equal to the scenario. (i.e. in a Battle PL, the commander is on one your Battle level ships, you choose which)
For every activation over the Fleet limit, you suffer a cumulative -1 to your Initiative
(This is the anti-swarm idea, but still granting a fairly large number of ships).
2) Shooting phase: you roll for Init in the shooting phase as well as the movement phase. The winner may chose 1 ship to shoot first (ship, not squadron). After that, all firing is simultainious.
(The idea that you can have this tit-for-tat of taking ships out before they shoot is silly to me. The show is full of all sides opening fire and the battleground becoming this maelstrom of released weaponry. That said, the show is also full of someone getting that first shot that can make the difference. For example, the Shadow ship against the G'quan in season 1 [granted that was an ambush], the Narn and the Shadows fighting in season 2 ["fire Energy Mines!"], and the battle of B5 in season 3 [the Clarkist Omega firing on the one captained by the Asian lady]).
3) New Special Order: Get a Firing Solution! A ship can make a turn at the start of the shooting phase, before the Initiative is rolled. This is not an extra turn but 'holding' a turn. (the language isn't precise because I don't have the book in fornt of me). All normal rules for turning and special orders must be obeyed. (so for example, a ship that can only turn once, essentuially doesn't turn in the movement phase but 'holds' it until the start of the shooting phase. The ship also can't launch fighters) CQ check is 8 (assuming average CQ is 4).
(this one is a bit more rough but it allows boresights to not be screwed with the reduction of Init sinks from rule #1)
4) Redundancy: straight out of the house rules people have used.
5) Stealth: A failed stealth roll makes a weapon Inaccurate. All hits must be rerolled. If a weapon system is Twin linked, then it simply loses the trait for that shot. All stealth scores are increase by +1.
(Stealth is unbalanced, just frustrating, so the balance is the stealth bump).
6) Interceptors: The owning player chooses against which enemy weapon they will be used first, requiring the enemy player to roll that weapon first. If the player has interceptors left, he chooses the next enemy weapon agaisnt which they will be used.
(It annoys me to see minor weapons burn up interceptors. If you have sufficiently advanced computers that can target relatively miniscule targets moving at very fast speeds, you could also heve them zero in on specific weapons of the enemy ship)
There you go. I have a feeling most people won't like these ideas, but for me it makes the game have a less clunky feel.