Silvereye,
As I currently understand it, all you are really giving up when you select a Great House fleet instead of a main fleet is access to the Octurian, Liati, and Adira (of which, really, multiple Primus are in general better), access to Sentris (and here, Raziks are better), and access to only 1 Primus or Tertius (and really, with the Sulust and Prefect at Raid, this isn't any serious loss, either.), and (probably most importantly) +1 initiative bonus. That just isn't giving up much of anything. So, what you're giving up isn't a ton; we shouldn't get a ton back in exchange, either.
The 1 Battle does create a fleet hole, however -- you won't be buying any Balavarix anytime soon. So, auxiliary craft and aux craft defense are new issues. This was the first idea when I went writing.
My thoughts:
Ardo: Bonus -- yes, they are Havens, but you're getting one extra FAP per battle for free. Even if you just use them as initiative sinks behind terrain, this is pretty huge. Against races with shorter-ranged non-turret weaponry -- some 3rd Age EA, Dilgar, Drakh, Abbai -- and those with Boresight restrictions -- 3rd Age EA, Crusade EA, Drazi, Narn -- this is a very big deal. So, you can't get this advantage, as bad as the Haven is, without a significant price. The Maximus isn't a bad ship, and, with initiative sinks to help out, the Vorchan might actually be a good ship. I just kept the abusive beam ships --- and not all of them, the Darkener is still out there! -- off the table. In exchange for a whole extra FAP point, Ardo gets an absolute steal. Ardo might actually still be overpowered in this version.
Orestres: The more I read my Sabotage rule, the more I dislike the implementation. Stupid idea. I just don't want to really mess with some races without recorse -- consider a Pak ship that might never be able repair a critical. In campaigns, where high CQ ships proliferate, this gets pretty harsh. And remember, we're only really giving up +1 initiative here. 1/3 of the fleet experiencing trouble is problematic. Perhaps replace the Sabotage critical effect by being able to, once per game, cancel or remove the effect of any one special order on any one ship, in addition to the CQ 3 on a 1-in-6 chance?
Another thought:
Superior Intelligence: Orestres doesn't just gather intelligence on opposing fleets, but also on individual captains and tactics. It allows them to force other captain's hands by provocation. During your movement, you may choose to move 2 activations' worth of ships at the same time. In exchange for this loss of initiative sink, you may select which of your opponents ships must move next, instead of your opponent choosing. Selected ships in a squadron may break off the squadron at this time; the whole squadron does not have to move. You can do this once per 2 FAPs in the scenario (3 times in a 6 Raid or 6 Battle fight), rounding up.
Kodiro: You're getting something for free, Breaching Pods in hordes. Pods normally stink, but in big waves, they are actually interesting. You'll struggle to get them past fighter escorts, which I'm fine with. I definitely do not like the explosives rule -- why doesn't every race fit them? Capturing is enough VP on its own. As to the disabling devices --- if the slaves knew they had them (they would), why would they even try fighting? And some ships have shields, the remote control might not get through. Finally, we have just seen a group of any slaves just commandeer a Warship. Memories of Narn insurrection might suggest the best treatment is the elimination of the threat once and for all -- Maker knows what slave might be hiding in some air duct, marked up as dead during the chaotic fighting, and going to run commando through the ship. Better safe than sorry. But, mostly, I did it for balance.
Mollari: Well, I was hoping as a Raid selection it wouldn't be bad on the table. The range is 30, it's now Raid, you could operate next to the base and force something to enter into range or suffer long-range Battle Laser plinking. 10 fighter flights are something you normally need to buy a Balavarin for anyways (and that's provided you get them all launched!), so that can help against EA. I added some extra incentive by giving some access to Rutarian goodness, something that you don't normally see right now. Eh. I was thinking in campaign settings, the basemight be too powerful (remember -- we're only giving up +1 initiative and some other things we can easily do without), so I was thinking of boosting Mollari's Base expense from 5 RR/turn to 6 or 7 RR/turn to make up for the relavite purchase savings --- from 40 RR, which can be hard to amass in one turn, to 30 RR.