Judging from this image:
http://www.moddb.com/mods/star-wars-ascendancy/images/updated-faction-select-screen#imagebox, there are two factions left after Hapes.
I am almost certain the Yuzhang-Vong are one of them due to the unique gameplay they could bring (There also exists some files for them in the folders of the mod); as for the other I hope it is the Ssi-ruuvi Imperium so the remaining two factions would be polar opposites of each other with the Vong being focused on individual very powerful units and the Imperium on massive hordes. Plus both would be completely alien factions which would be refreshing.
If the Hutts were implemented I think they would work best through Sin's vanilla mechanic where you bid on pirates so they attack you enemies as that would model them well in my opinion.