What game had the best guilds? The 'you're my only hope' Skyrim, the 'cool theme park' Oblivion or the 'typical guild job' Morrowind?
I would say they all sucked fairly equally, for different reasons.
Morrowind's sucked because nothing you did in them was worthy of advancement, it was shit those guilds regularly outsourced to other mercs, and often amounted to literally "pick flowers", or "ask people to donate money" and were about on par with Skyrim's radiant guild quests in terms of depth, but without having systems in place to make more of them. On top of that, the way you advanced didn't make much sense either, it was like you just went up to someone and showed them your stat sheet, which wouldn't actually exist, and never did they really make you DO anything to prove you had the skills you said you did.
Oblivion was better in that they actually had some attempt at a plot, which actually made getting named guild master somewhat logical, but they were so pants on head retarded, just like everything else in Oblivion, that it fell flat. On top of that, it didn't rely on the magic "stat sheet" to gain advancement, it was more "people actually saw you do shit", so it made more sense there.
Skyrim had better plots then Oblivion's guilds, and generally had more instances of "you actually have to use the skills you are supposed to have for this guild" then Oblivion did(I actually had to use magic in Skyrim's College questline then at any point in Oblivions of Morrowinds Mages guilds) but were ultimately let down by the fact they were short as fuck. Likely a result of trying to appease the complaints that Oblivion's guilds had too much padding, and too little plot, so they just went "all plot" and sucked because some padded is needed to make them not feel rushed.
they all kinda sucked and weren't very believable.