I think independents vs. factioneers aside, much of the issue is about factions being too powerful/elitist, which may have its own merits and enough people already touched on.
Rather than making factions more powerful, it might be a good idea to make them more specialized, or at least more accessible.
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By this I mean, trading factions (Universal, Republican, etc.) could receive a bonus on buy/sell prices at some small rate (perhaps 5% over non-fac-ID'd traders), while weaponry comes at a 5% tax.
In the same boat could be House Navies, which could receive 10% discounts on the big purchases (cap ships/high tech guns) from their own house shops. (I'd balk at giving them a tax right now since the balance is still off, but it could be on things like ammunition.)
And pirates could be given a 5% discount on equipment purchases with valid ID at their bases (since, I mean, who thinks pirates are going to pay full price for a standard gun available on Manhattan?), but a 5% tax on buying new ships.
And this could be applied to specific player factions, too... if you want to strengthen the 'official' ones. (Ie: Universal ID gets 5% price bonus, *USI* gets 7%; Navy gets 10% off Class 9+ guns, [LN] gets 15%).
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Give something, take something... it's an economic tool to help push players towards choosing factions (even if not player factions) to get experience with, and if you tweak it right (as in the Navy above), it can be a tool you can use to address some balance issues.
It's not at all different from what happens with every update and the minor market price adjustments, but if it took place on a faction level, it could change how people value being in a faction.
It doesn't address the guys flying around ignoring RP and just messing thing up... but hey, you could put big taxes on the Civilian ID to make people want to put the time in and move up. If someone is about to F things up and not RP right, they won't be up for putting the extra time and effort it takes to get past civ.