Just pointing this out... Oblivion's guild quests were much more rich and you can tell a lot of detail was put in them, whereas in Morrowind quite a lot of the quests were "fetch this". This is why Oblivion had less guilds. They put more work into them. I say this as a Morrowind fan, so don't think I'm biased.
I say as an Oblivion fan that Morrowind was better!
Seriously though, I don't think the guild quests were lacking in detail at all in Morrowind. They involved politics more instead of the crazy scenarios of Oblivion (Mages Guild comes to mind first, I kinda like it when the side quests aren't threatening the world...leave that to the main quest). The Great Houses of Morrowind were especially good in my opinion. In fact, the more I think about it, the more I realize how good Morrowind's guild quests were! Its true that many of the quests, especially the beginning ones, were "fetch" quests, but that is how your beginning quests SHOULD be! What have you proven so far, right? Oblivion wasn't too different in that regard really...
In the end, I just liked the choices:
Morrowind-- Blades (Main Quest), Fighters Guild, Mages Guild, Thieves Guild, Imperial Legion, Morag Tong, Imperial Cult, Temple, Great House Hlaalu, Great House Redoran, Great House Telavanni. There are also the three different Vampire Clans (Berne, Aundae, and Quarra) that were hard to find but oh so rewarding
Oblivion-- Blades (Main Quest), Fighters Guild, Mages Guild, Thieves Guild, Dark Brotherhood, Arena (I would only count this if Morrowind can count the Vampire Clans).