The helix, looter or seeker would make good replacement options for the coat-rack'o'doom (hunter)
Personally I like the idea of varied shadow ship miniatures, but they shouldn't have different priority levels. What is ostensibly one of the oldest of the first-one races has no place fielding a skirmish-priority capital ship when a 'mature' one-crew primary vessel is Armageddon...
I like the idea of ships with more personality; given the whole ship is one organism, you shouln't have refits, but you can perhaps pick up experience and favoured tricks.....if anyone's seen Battlestar galactica, I'm thinking of the cylon raider 'Scar'