I'm a huge FTII fan, and I know someone worked up K'ilrathi ship designs at one time, but worthy of mentions are G.O.B.S. and A Sky Full of Stars. The first is totally free as far as I know, and the second has a simple rule set available for free, with a larger pay version on RPGNOW.
There is/was a Space Cruiser Yamato based game from Musashi Enterprises, but I found it a bit daunting from the buckets o' missiles point of view.
Unfortunately, it's been so long since I watched someone playing WC, never played myself, I'm not sure which system to suggest.
Doug