I have been giving this one a lot of thought lately. I want to see fleets that allow for captured vessels which only makes sense given the rarity of space craft, but at the same time I don't want to see the "feel and Style" of the various Noble Houses, League, Church, Imperial Fleet, Barbarians and Aliens diluted. Which as Msprange pointed out is exactly what starts to happen when even a few ships from another fleet are added. However this is not an obstacle that can't be over come.
I think one things we might do to keep a strong theme going with in a given Faction fleet is to remember that the crew are all from one house. They were all trained the same and are commanded by officers and Nobles who studied at the same academies. When Mongoose gets around to adding Legendary Captains and Admirals to the game I propose that you only be able to use officers from your faction. Each faction's officers should have access to a unique style of abilities that are there's alone. This way when a Hazat Cruiser is under the command of a Hawkwood Admiral the crusier clearly remains a Hazat design, but the bonuses and extra abilities provided by the Admiral are uniquely Hawkwood. By doing it this way, and limiting the percentage of points that can be spent on ships from other factions, We can maintain a strong faction "feel" to a fleet without restricting the selection of ships to just one faction.