2TarNutz: It took some time, but I've read everything. One simple objection is: 1) there are no nomad bases anywhere (and if there were - what NPCs? what rooms there) and 2) not so easy as it seems from your post. This way players could gain neutral rep with everyone, thus having access to all Sirius including nomads.
I'd agree that this matter requires some more research, but for 4.81 I'm satisfied with reputation modifiers as they are.
To gain better reputation with Zoners, you could use LWB, Unioners, GMG, IMG (IMG in particular)... they are all slightly allied to Zoners. As for Zoner missions, I don't know exactly why are they not giving missions... guess the reason is that they are neutral to all surrounding factions. For now, I'm rising reputation modifiers for Zoner guardians, so that changes in Zoner reputations will influence guardians faster. Then, I'm removing reputation requirements for all equipment on clan bases. Hope that's enough.