As we can tell, guilds are clearly separately designed in oblivion as they do not interact at all, which leads to strange shenanigans, such as the Archmage stealing from himself.
However I can understand that, from a programming and project management point of view, it is much easier to develop and test them as independent modules. Too much interactions between modules (guilds/faction) makes the whole thing very complex and much much harder to test.
If TES is built on story telling, such as JRPG or other linear RPG then they should go out on a limb to make sure each module fits tightly with other, since it's all linear. However TES is built as a open world, this means interactions between modules would actually go against the world design principle.
Case in point is Fallout NV, the game was mainly lambasted for two things, bugs and having a small world. It is mayhaps only half the size of fallout 3 as most POI on the map were uninteresting abandoned shacks and most of the houses cannot be entered.
The main reason is because they had to spend so much time developing and testing and debugging the main quest with all its alternate endings, factions and complex interactions.
So my take is this, while it would be interesting to have interplay between MQ factions (empire vs rebels), to go too deep into it (winterhold vs thieves vs campanions vs DB vs bards) would actually reduce skyrim from open world into a more linear multipath game. That and also the new release date will be 12-12-12.