Nakalim make the Sophons Gameplay affinity near worthless, solution is to give the faction trait that gives them the first two eras of tech give unique versions of the tech that don't affect omniscience.

or add 10 more players to the map to minimize effect. hehe

We've had other people point this out and I discussed it with the designers back then. This is intended. It will hamper the Sophon in the early game, but if they catch up to the Nakalim, it will be hard for the Nakalim to keep pace after that point.