I think this should be extended to all the factions and not just the guild.
I also think that faction reputations should have bleeding effect as well, where reputation gained with one will have a smaller effect in another. (eg. Gaining 20 reputation with a town citizenship would also increase your reputation with the town guard by 5.) This would only apply to groups that are friendly with one another and would only be applied to quests which affect the group as a whole.
And, gaining reputation with one group could hurt your reputation with another, for instance, if the Thieves Guild asks you to rob the Mages Guild and you do it, you will lose rep with the Mage Guild. Or, I think there will be two mages type guilds based on The Infernal City, if you gain reputation with one, you will lose reputation with the other. And none of that joining every single guild like in Oblivion.