Juniper's Twin Lamps: As far as I'm concerned, this is THE twin lamps mod. In spite of its age, it provides multiple ways to proceed through the main quest (giving you the chance to completely ban the slavery on Vvardenfell, if you wish so), choices with appropriate consequences and not the usual fetch quests which are unfortunately so common in vanilla Morrowind.

Then, if you plan to play as a Telvanni, these two are pretty much mandatory:

Rise of House Telvanni and Uvirith's Legacy: the first one adds 20-something quests when you become Archmagister, providing lots of choices with sometimes world-altering consequences
The second one *dramatically* enhances the Telvanni stronghold, adding tons of quests (again, it often allows you to make choices on how to proceed). Unfortunately, RoHT and Juniper's Twin Lamps are "conceptually" incompatible if you play them together, since for instance you could find yourself in a situation where you have banned slavery with TL, yet you're still dealing with twin lamps in RoHT as if nothing had happened.

Other recommendations:

Havish: best thief quests I've ever seen in pretty much any RPG I've played, the original Morrowind thief questline absolutely pales in comparison. Not to mention it's strongly inspired by Daggerfall (and it shows, especially in the layout of the main city), and that's a huge plus for me.

Booty Island: another great mod by JOG - not exactly lore-friendly, but still very much worth playing.

Lothavor's Legacy: story based mod with a huge focus on NPC interaction and extensive branching dialogue trees for each one of the six NPCs you meet (they all have their own, random, schedule and interactions - for instance, they react if you get too near when they're sleeping).

LGNPC series: gives many of the uninteresting NPCs you find in the cities a personality (therefore giving you a reason to talk to them), as well as adding many well-done quests. LGNPC Pax Redoran completely overhauls the Redoran faction.

Tamriel Rebuilt: the first map has more than 100 quests, many of them with multiple paths to completion.

Archipel de Pertevue: if you can read french and spend some time to make the plugin compatible with the english version, this mod is an absolute must. It adds something like 200 quests, multiple conflicting factions, a whole town you can build and then manage with lots of inventive quests (for instance, in one of those quests, if you make a stupid decision you have to stand a trial!) and many jaw-dropping scripted effects (a ship sinking in real time)

Iredior Conspiracies: this is a beta of a mod which unfortunately was never finished, but it's truly a hidden gem: it adds a HUGE city, multiple new factions, many inventive quests which often allows you to make choices with big consequences (for instance, there's this quest where, if you are a member of a faction and you make a particular choice, you can have the Mages Guild banned from the city - then there's the whole political main questline dealing with the assassinations attempt on the king which allows you to take sides). As I said, though, the module isn't finished, is buggy and many of the quests can't be completed unless you're willing to use the console.

This, of course, isn't a comprehensive list of quest mods, since there are many other good ones - I'd advise you to search on PES and/or on Morrowind Nexus (that's how I found Iredior, for instance).