I always though some of the guilds in morrowind were kind of weak at times, The great houses were great for there conflict and that is what morrowind struck me as, a game of power struggles. so i have made a list of ideas to make it better, but i Just got skywind to load on CK and im trying out for clutter and random placement things. So i really hope to get a bit of help with this.
1
Thieves:
The thieves guild in morrowind confused me, in daggerfall they where hidden, and they came to you after you committed a crime, but in morrowind they are in the open. They brake imperial law and they are not protected by house Hlaalu like the Camonna tong so they would be busted fast. so making them more hidden would be important to lore, even oblivion know this.
Next the Cammona tong should be a joinable guild, so the revelry can be seen differently, and when the theives guild is stealthy the cammona are more thug like. and it will put you in good with house hlaalu.
2.
Slavery:
Slavery should be updated so you can join the twin lambs and go on quests to free slaves, or join Dres slave traders and and capture escaped one.
3.
Assassin:
The dark brotherhood should be a join able faction. maybe the same way in daggerfall, or oblivion, if you kill so many innocent people, or you have to find Severa Magia. but that would mean they could not attack (for Tribunal) because you're part of the guild so maybe the morag tong could attack instead, it would mean you cant do the hunt the dark brotherhood quest.
Or during the hunt the dark brotherhood quest Dandras vules recruits you because he is impressed with your work.
So dark brotherhood quests would be more stealthy and high risk because you are not legal like the Morag tong, and if you are in the Tong you are not allowed in the brotherhood Vise versa.
4
Werebeasts:
Maybe add werebears to solstheim, but it would be hard to. but if it were added it would be cool and lore friendly

Would just require designing
Would just require designing then making a quest with CK and scripts. Not hard stuff to learn if you want it badly enough. ;)