Everyone go and grab your reading glasses.
IIRC, the Civil War was going to be much grander. For instance, being able to lay siege to all cities, instead of just Whiterun (the game data files still include unused debris and object markers for that purpose). I believe it was intended that you could gain and lose holds over time. There's also unused data and script comments about other incomplete quests, including one for getting a giant to help by befriending it with a painted cow (oh, the fun that could be had by seeing a giant stomp into battle and send Stormcloaks into the stratosphere..). For some reason, I think the Civil War wasn't even going to be completable and instead was just going to be a constant back'n'forth with losing holds over time and doing quests to retake them, but I'm not sure if that was actually going to be the case, or if it's just something I heard somewhere else.
The biggest problem with the guild quests was that they were short, and the story was rushed and/or anticlimactic. The College, for instance, ends when it felt like it was just getting started, the Companions don't have you do much except kill some "special" bandits and some Hagravens. They're short even by Oblivion standards, and Oblivion already felt like it was rushing things at times. Also the railroading: you must become a werewolf to continue the Companions (can't tattle on Aela and Skjor for an alternate path siding with Kodlak, and can't even continue doing Radiant Quests once the non-choice is presented)... you must serve Nocturnal to continue the Thieves Guild... you must join the College for the main quest*, etc.
It definitely feels to me like the Radiant Story system was supposed to play a much larger role with the guilds -- not only in extending the quest lines, but also in providing alternative paths and keeping guilds going after the "main" conflict -- and they had to scramble to get something hand-done when they realized they couldn't get it working in time.
One of the bigger features of the Radiant Quests is to be able to psuedo-randomly select actors, locations, and items for a given quest (where a quest can be something as small as a guard trying to talk to you, or a barmaid/store-clerk tending their station), which could even be weighted or modified based on any of the innumerable stats the game keeps track of ("Bunnies slaughtered" is just the tip of the iceberg). Such a system could've been absolutely stellar for emergent storytelling and gameplay, if they had the time to get it working.