How about this, diffrent abilites for Omni/Clan/Neutrals. So that they are not so cut and paste. Have the clan engineers more of the, "find a part disasemble it and make it into something new" while the omni would just make new items. So in effect you would give the clan engineer a bonus to his B/E and the omni a bonus to his N/P. I'm not talking about screwing up high level characters....I'm not talking about taking anything away. ADD bonus's based on your fraction. Omni more of the scientific aspect and Clan more of the back to the earth type aspects. Make it so that it's more attractive for MP's to choose clan. Make it so that it's more attractive for NT's to choose Omni. You would actually have some deffinition to the game. Yes, you'd still have characters who switched sides for a reson i.e. roleplaying. But the majority of players don't roleplay. You'd encourage this by making the sides more attractive to certain types of characters.
Just my 2 cents, don't flame the messenger.