My only thing is that I've always thought the Nomads would work with the Phantoms over the other humans... Afterall, their goals are the same and the Phantoms are a smaller force, in general. Phantoms use stealth, fear, and subversion to continue to exist, while humans can simply use brute force. For example, if every house were put together against the Phantom Empire, we would have no chance. There's only two or three battleships in our fleet, while there are a hundred in the Houses. That's the reason the Revenant is placed where no large fleet could actually enter (after having to survive Outcast or Corsair fleets only to be bottle-necked on their way in). As a matter of fact, there are actually Nomad ships protecting the jumps to Omicron-82.
Phantoms have also helped Nomads in the past, remember the NCU incident where the HMCS Magnificent crashed into Manhattan? Phantoms allowed Nomads to gain control of that ship by sabotaging the Nomad Containment Units (NCU). For the longest time, Phantoms were the only ones to ever have contact with the Nomads, without hostilities. When the Keepers came around, that disappeared because someone thought that the past doesn't matter (or just forgot or didn't know).
Addendum:
Also Phantoms aren't inheritantly evil, either. They fight for galactic peace under the rule of the C'Tan. The Enlightenment process makes you completely under the power of the C'Tan while maintaining whatever other freewill you may have. For the Phantom Empire, it was necessary for the enlightenment to make them excessively violent. Like I said before, the Phantoms only exist because of fear and stealth.