So, I think Dark Brotherhood as joinable faction should be considered. We can easily forget the part in which Mournhold part of Brotherhood tried to murder us. Dandras Vules acted on his own and was in conspiracy with Helseth, was blinded by the money and this writ should never be accepted because employer never performed Black Sacrament or something in this mould if Black Sacrament is purposely removed from Tamriel Rebuilt's lore. To avoid confussion we should get choice to join Dark Brotherhood only after Dandas Vules is dead (you should probably have possibility of joining only DB or only Morag Tong, but we know that Eno Hlaalu was willing to work with former DB members as Tsrazami, so it's not a must). This can be done with sleep interruption that drops a letter close to us (black hand, we know, etc.) detailing how to meet up with this secretive guy who will happen to be DB member.

Since it's Morrowind and Dark Brotherhood is less significant guild here than in other provinces, its questline shouldn't be long, maybe few quests dealing with some blank murders and then few quests dealing with Morag Tong (so pretty similar to Morag Tong actually, would need good writing to make things more interesting) and we shouldn't be able to get the highest rank just like in Blades or Ashlanders factions.

Of course its questline might be more significant and include some of the following: killing Vedam Dren, killing whoever Helseth doesn't like, killing Helseth (I believe most of the Tribunal expansions is going to be remade and this is good way to remove those weird things introduced in Morrowind expansions like quasi-immortality of Helseth, quasi-immortality of Barenziah who happens to have the best destruction spell in history of TES), killing Barenziah, killing pretty much anyone important if you will find this interesting from gameplay and storytelling perspective.
I think DB being "Morag Tong archenemy" would be better than "kings, queens, dukes, princes and emperors murderers guild", though.