I have been thinking about the guild system lately too, but was thinking in a bit of a different direction. More of the mechanics of the system could be changed to make a better RP long term, and more RL like at the same time. NPC guilds may have their place as well as the player run ones which I cannot see stopping.
1. Players should be able to enter multiple guilds at the same time. This would better enable both the alliance capabilities, especially in times of war, and the ability to RP a spy or evil character trying to corrupt the good, etc. Or a good character trying to infiltrate the the and expose the evil.
2. The guild affiliation display should be individually switchable so others can or cannot see it as determined by the character. A good character trying to infiltrate an evil guild (or the other way around) would be rejected if known even OOC to be the opposite.
3. It would help also to have your own name display switchable for the same reasons. Someone covered up wearing a hood and sneaking in shadows is readily revealed by the big name tag. Turning name tags off also could help with the role play understanding (should not need this I know) that not everyone you come up to is someone that is known and to be addressed by name. I should point out that turning off the name should not remove the name from the stats window when selected. this would enable a thief to be followed, etc. in spite of the possible computer glitches.
Multiple guild associations would allow the use of both NPC guilds and player guilds without removing the benefits, quests, or RP possibilities of either the NPC guilds or the player association guilds.
I did not research the forums, and maybe these ideas were already given in someone elses post. I just saw this post and though I would my 2 trias.