Two things I liked about Morrowind's guilds; Level requirements and Guild conflicts.
Level requirements make sure that you are proficient in certain skills if you were to advance in a Guild. For example, you need to be skillful in magical areas if you want to move up in a mage's guild.
Guild conflicts were awesome, because it gave the game replay value. One could not join every guild in one play through because certain guilds were enemies and it wouldn't make sense to be in both(eg. The Great Houses). It wouldn't make sense if someone was part of House Telvanni and then get a quest from the Mage's guild to kill all the Telvanni councilors.
A new concept; Gaining responsibilities as you progress in your faction.
As you progress in the faction, you should gain responsibilities and benefits. Perhaps in the fighters guild, at a rank near the top like a captain of some sorts, you can gain control of the fighter's guild in a certain area. Control of that area of the faction would come with regular challenges from other fighter's guild members, who want to take control of that area, so they challenge you to a duel. That being said, if someone doesn't want to be pestered with the constant challenges they receive, they don't have to control they area at the required rank, but can choose to. With control of the portion of the guild, you would receive a steady flow of income and would be able to have members in your area become companions.