What about faction quests on Vvardenfell Island? The 3 houses, the Guilds except fighter's guild, the religious sects like the Imperial cult and tribunal temple, etc.
To bad some skills are useless like the ones where you make one kind of monster non hostile like Giants, Orcs, and Dragonlings.

I didn't finish everything. However I did most (like 90% or something) of mages guild, imperial cult & temple quests. Also about 50% of the rest of the guilds stuff. No problems there.

Edit: Oh yeah, and finished telvanni. Forgot about it.

Agreed... unless you only plan on playing the game once.
In that case, you mightest well make the experience as great as possible.

That's the thing tho, you can't possibly know what will make the experience as great as possible. The combination of mods for perfecting the game is going to be unique for every single player - given the length of the game, the best thing you can really do is to pour a couple of hours into vanilla and then decide based on that.

For Morrowind, try not to change too much of the base game. I like to stick with quest/guild type mods. Combat Enhanced (the one with the combo moves) was super awesome though, so probably get it if you can.

Suran Underworld and Illuminated Order of the Invisibles were great. I liked Beyond YsGramor, but it also conflicts with Tamriel Rebuilt (maybe not so much anymore?), so it depends on your tastes. I haven't the slightest clue what substance TR really has so I never really tried it beyond one time.

I'll say try not to change the graphics too much, as my impression of the graphics mods was that they mostly conflicted with everything, though some of the face mods are fine (don't remember specifics).

Also, make sure your computer is packing a punch, Morrowind will slow it down like nobody's business when you get carried away.

You mean like Skyrim? :P

I would...actually be inclined to agree with this viewpoint, with the exception of the bug fixes (Morrowind Patch Project and Morrowind Code Overhaul, both listed on the UESP wiki) Akhliber's suggestion in post 3. For the latter, you probably shouldn't read the description as it contains spoilers for later in the game, but suffice it to say that due to a poorly thought through idea, one of the expansions - aimed at high level characters - starts much earlier than it makes sense to either in character or from a balancing standpoint. By the time you find out, it'll be too late to correct it (without restarting), so you'll just have to take my word on this.

Agreed^2.
I purchased the Xbox version long before purchasing the PC version, so I had the pleasure of enjoying both the vanilla game and the modded one, which is an entirely different experience.
You hear that, Niggles? Enjoy the game before installing anything other than patches.