I see how the Nomads going neutral could be unbalancing if everyone else was neutral or positive: Freelancer without enemies is boring. I have a solution.
I was thinking that if the Order had big positive Empathy with all human factions one way or another and a negative Empathy with JUST the Nomads, and the Nomads had negative Empathy with JUST the Order (and was otherwise directly neutral with all other factions as far as Empathy's concerned), then the only way to get the Nomads to go neutral or better would be to shoot down the Order, which would cause all the human factions to hate you. If you're afraid that they could just get Neutral standing all around, then go ahead and pump the Order's positive empathy with the humans to double or triple their negative emapthy value with the Nomads. A ratio of +.40 positive Human and -.10 or -.05 negative Nomad for the Order should do it: by the time you got the Nomads to stop hating on you the Humans would be out for blood.
Then again, shooting down ANYONE if the Order has Positive Empathy with all Humanity would piss off the Order quickly... so you'd have to prove yourself to them before you could dock at their bases by fighting the Nomads in Omicron Alpha, Omicron Gamma and Alaska for a while, at least until they went Neutral. Which makes sense: secret societies often require initiation rituals, and as secretive as the Order is, most humans wandering into their territory would probably be considered hostile until proven otherwise (the Nomads DO possess people after all). Positive Empathy does not equate with stupidity. Plus this encourages those who've moved on to fighting Nomads to leave their petty quarrels with Human factions behind in the face of more sinister foes: involvement in such petty quarrels is frowned upon by the Order as a waste of time and resources. Besides which, the Mafia has a saying: "The Eagle doesn't hunt flies."
Shooting Nomads would only buy you points with the Order in such a case: the rest of the factions would continue to hate you or love you regardless of your Nomad hunting. Shooting down enough Order pilots (and ONLY Order pilots) would buy you points with the Nomads, but at the cost of every friend you had in Human space. Empathy, BTW, doesn't trickle down: shooting down Xenos gives you bonus points with Liberty Police AND Liberty Rogues, Outcasts, etc. The fact that the Rogues and Outcasts like your activities too doesn't make the Liberty Police any less grateful. And then you don't have to bribe anyone, etc to get the Order to like you. The only "problem" would be that the Bounty Hunters wouldn't attack the Order anymore if they were positive along with everyone else.
If you want the Bounty Hunters to continue shooting the Order, that's easy. If you left the Bounty Hunters out of the Order's little Empathy circle (but didn't make 'em negative like the Nomads, just put 'em at zero) then you can leave the "Rep" value negative with the Order. Then, shooting down the Order won't piss off the Bounty Hunters, but won't make 'em your friends either (everyone else, of course, will hate your guts). Meanwhile, the Bounty Hunters will continue to attack Order ships and bases. I don't know if you could still land at Sheffield in Manchester or Deshima in Shikoku with neutral or better Bounty Hunters and everyone else hostile: my guess is no, because they're "lawful" (despite how often they attack House capital ships in a mistaken attempt to "rescue" the officers aboard).
About the only thing I can think of that might imbalance this system and allow someone to be friendly with Nomads AND Humans would be to bribe factions while attacking the Order here and there: you might be able to save your rep with a few factions while getting the Order to hate your guts and the Nomads to lay off. You could easily fix this, if you leave the Rep column (not Empathy) as NEGATIVE for all factions against the Nomads, so bribing ANY faction would piss the Nomads off, undoing your attempt to butter them up by killing the Order (which of course pisses off the Humans you wanted to bribe in the first place). With this consideration, any way you cut it: if you work for the Nomads, you're an enemy of Humanity.
How's THAT? With this solution, you COULD go Nomad, at the price of your Humanity. Going Nomad would make it a pain in the ass to dock anywhere in the House systems: the Omicrons would be your new home. Makes it a bit interesting in the late-game, too: after you've gotten rich fighting the House's conflicts and moved on to the Order/Nomad conflict in the Edge Worlds, you could then turn against humanity for the promise of advanced technology only sold on Nomad bases to Nomad friendlies. You could even have a change of heart and fight the Nomads again afterwards to regain your good name with Humanity: adds a whole new dimension to the gameplay with the tweak of two factions' Empathy sets (and perhaps one Reputation set). Besides which: what's the point of having bases you can't dock at?
