Hey, just caught up on your mod, and it looks great!
While reading this, I got a couple of ideas for the wraith tech tree:
1. Improved Hibernation chambers (Increased fleet capacity?)
2. Anti-beaming counter-measure (This was cannon, and could be used to dampen the effects of a nuke beaming from insta-kill to just damaging, would help balance the massive overkill)
3. Clone-facility (Just a random idea for incraesed planet population growth)
4. Improved FTL drives? (Well technicaly they stole these, but its an option)
5. Subspace Tranmitter (A scout ability used to tag ships to scout planet locations?)
Well, thats all I can really think of for the wraith.
Also, i had this idea of how Michaels hybrids could be a sort of pirate faction, but then again, it might not work out, just thrown this out there. Anyways, good luck with your mod, ill be checking by once in a while to look at your amazing designs 