1. Discounts by Commodity (This could require a new Ageira PFaction ID)
-To touch on this with my own idea, what if creating a alternate set of ID's for Player Factions, I know the Guard ID's are that to some extent but maybe make them harder to get or only attainable to Player Factions. Though some modifications might have to be made as indies shouldn't require Guard ID's to do things the NPC faction can do but they wouldn't be able to get the bonuses.
2.Faction ships
-I really liked this idea but a problem arises when you take in account the fact that their are multiple factions per NPC faction and what about Custom Factions, or the ones that are more unique.
3.Faction Weapons
-This one was reasonable especially if you make Codenames belong to Indies, it would give a nice bonus but not break or give too much advantage to players it could also make for good RP selling weapons and factions having to take in account how these weapons are used. IE... "Why the hell are these ships attacking me with your Weapons?" Thus creating roleplay by creating some interesting diplomatic moments. (I'm a sucker for Political RP/Diplomatic RP)
4.Make Large Capital Ships Special RP (My Idea)
-I'm against having Factions OOCly having control as it calls for problems should OOC Bias or dislikes occur what I do think should happen is make them all or at least the large Capital ships restricted to RP applications. On my other server, (Non Freelancer) we make all players require Profiles to be made to get passed Level 50. If they get an approved profile they receive a bump to level 80 and tokens in which they can get any item they want. The point? This allows regulation of good characters from LolWhat characters.
We all hate LolCaps and we don't want one person to decided who can get a ship and who cannot unless that person is a admin. So why not do this and be a bit more acceptable to those who are part of Factions as they are following the rules of the faction and are easier regulated. Indies are on there own but if your part of a faction your more likely to see LolWhat's get punished.
That's all I got for now but I think there are lots of good ideas on what can be Bonuses.