Well, if it is size and general development, then I'd say Zoners.
As for storyline, I would say both the Order and Nomads, Wilde and so forth.
Let us not forget Gall...oh right.
House militarily also have expanded and there is much more information about them now. Independents and Freelancers are more defined. It just keeps going.
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It depends if your talking about Vanilla Factions or ones also added into it.
If by that than I'd say the Coalition, it's got history pre-dating the Zoners, they went from a Power dominating the Alliance to a bunch of ragtag saboteurs to a Mini-House and a fearsome reputation.
If your talking Vanilla than it's definitely the Zoners because frankly, they went from a bunch of 'crazies' living in between houses trying to survive without the major governments to practically a Mini-House in itself with a story of their own that is expanded upon in the mod.
It's obvious that the most developed faction is actually Ordur. From one cloaking BS they became an Ossie spamming power which gets hunted by another strange thing called Core and now they have their own systems nearly acting like a house and such.
But it's empty qq.
Needs a central place to swarm around or people get bored.