Unveiled Masters has a significant number of prestige classes for illithids, around six I think. One is specialized towards fleshcrafting, a illithid talent described in the book. Also present is the Warrior of the Violet Line, a fighter-type for those martially inclined illithids.
If it was me, I would start them out as straight MM illithids, and then let them take class levels as they advance. Probably Fighter, rogue, wizard, monk, ranger, and the psionic classes. Definatly not barbarian or druid. Illithids in my campaign are atheistic, so no clerics. Probably no sorcerors, they don't have the right feel. Definatly have their own groups of thralls. An Ars Magica style game would be cool, particularly when the thralls are unable to complete the mission and the masters must take a direct hand!
Threats:
1) Interfering surface-dwellers.
2) Meddling extra-planars who can outwait the masters.
3) Undead who are immune to the master's powers.
4) An ultrathelid is born to the colony, derailing their plans.
5) Other factions derailing their plans.
6) A neothelid from a nearby "lost" colony goes on a rampage.
7) Gith Attack!
Cool idea. The mind flayers are my favorate evil-guys, and a evil-Ars Magica game would be very cool.
