Star Trek Armada and Conquest Frontier Wars. The resulting game would be basically CFW set in Trek Universe. I would be willing to substitute CFW for upcoming Gemini Wars (but this would depend on the quality of that game, as it was not released yet, its difficult to tell) or perhaps Sins (but i would require some changes, mostly related to making the game more multiplayer-oriented).
Alternatively i could use crossover of Homeworld and Sins, again basically it would play like Sins set in HW universe. Frankly, if Relic at some point decides to make HW3, i hope it will be something along these lines.
EDIT: Oh, now i see, the HW + sins was already proposed several times...unsurprisingly
i wonder if you want it to be under the same specifications as me, or would you like it other way around? I mean play like HW with Sins races?