Please let us have some mutually exclusive guilds, like Morrowind's Great Houses. It adds so much replayability to the game to have guilds that you can't join because of a choice you made earlier to join one of their rivals.
I agree, the Great Houses of Morrowind and the huge re-playability factor, are what make Morrowind my favourite game ever, even though I was introduced to the series by Oblivion. I hope that Skyrim has it's own Clans like the Great Houses. We know there are 9 holds, but maybe there are a few clans that encompass multiple holds e.g. Haafinheim (Solitude) and Northshore (Dawnstar). From looking at http://i1126.photobucket.com/albums/l615/Duruza/Skyrim-map.png, which seems fairly official, I would think The Rift and Eastmarch; The Pale and Winter Hold; The Reach and Falkreath Hold; and Whiterun; as the five Clan alliances.
On top of this, maybe some kind of freedom fighter/terrorist group, fighting for freedom from an 'evil' opressive Imperialist force, but who use methods which seem evil in themselves, such as the kidnapping and killing of innocent civilians. On the other side of the coin you could work for the Imperials to crush this organisation, forcing the player to decide upon joining the lesser of two evils..
This is very similar to an idea I had for an organisation called "The Brothers of Skyrim". Basically I had them as "An heroic group of Nords and some other residents of Skyrim, that have banded together to fight for the people of Skyrim. Heroes of the Oblivion Crisis in Skyrim, now they are divided and there is open conflict in the ranks over the future of the Empire. All of Skyrim watch keenly for the resolution of their internal dispute as it may foreshadow the future of Skyrim and it's place in Tamriel." Basically, the faction is splintering into three different factions, the traditional Brothers of Skyrim - who only want to see the best for Skyrim and, while they are truely noble, will not act on the new issues in the faction; the New Brotherhood - a fanatical group of freedom fighters; and a final new group of near-fanatical Imperialists who will stop at nothing to ensure that 'the new brotherhood doesn't kill Skyrim by making it the target of it's neighbours'. Basically there are several endings to the main questline, you can side with one of the fanatical sides, stay true to the old ways and take a corse of action either way, stay true and do nothing seeing the faction actually split and leaving you with the remnants (semi-failure I guess), or finally you may crack down on both sides and let the Clans and politicians decide the future of Skyrim - nothing really would happen then in-game unless the mainquest let you chose a particular side.