I think there should be a counter guild for every guild, for example a necromancer guild that stops you from the joining the mage's, or joining the morag tong that stops you from being part of the dark brotherhood. That'd make pretty replay value.
No, that's silly evil group vs. good group. I'd rather have various organizations like and hate each other, and sometimes sub factions in the organizations.
Also, for the love of Nurgle and Khorne, THE MORAG TONG IS NOT LEGAL! They are ONLY legal in Morrowind, and that is ONLY because they went to Vivec to allow continued and regulated operations in Morrowind. Outside of Morrowind, they're just another group of killers that will be killed. However, Morrowind went boom, and the dunmer driven out to places other than Morrowind. Hell, they assassinated a [NUMMIT] emperor for money. Do not buy into their crap. If given the opportunity, they would run their organization very similar to the Dark Brotherhood. They'd never admit it, but that's only because they became regulated hitmen, in a culture that approves of secret murder.