Official factions have something to say regarding the change in diplomacy, techcells or even some additional ship for a faction (if they lack it) - not to mention they have right to sanction characters or even entire factions (even if they bear same ID and IFF). These are things that unofficial factions cannot do.
However, I think people tend to exaggate, because official factions bear the great responsibility, both to the leaders and players - no matter, if that's roleplay, ooRP/iRP logistics or PVP abilities. Sometimes official factions can be hard to be in, because they require players to keep to ship restrictions (vide SCRA or 343).
