Late to the party, but I want to chime in with an endorsement for Wrye Mash as a mod manager for non-OpenMW setups. Wrye Mash Standalone is a bit limited compared to later iterations since you can't drag and drop mods to change load order--you have to manually enter the LO number. Minor grievance!
I've logged ~130 hours into my current (very heavily modded) Morrowind playthrough, which is based off the guide here on STEP. There are some minor compatibility issues with the guide (mostly armor/better bodies related), but nothing major. It's a pretty light-weight guide and everything works great.
I used the STEP forum guide as a base, but integrated mods from these mod lists/guides here:
An Alternative to MGSO: This guide bills itself as a comprehensive overhaul guide that does everything MGSO does and better. Lists all the original mods, or better alternatives. I highly recommend it. It also includes a few optional fixes for Vurt's grass overhauls (floating grass, grass on roads). Lots of overlap with the STEP guide, but lots more texture/mesh replacers and
GeeTee's Guide: A Steam community guide that uses MGSO as a base. I don't recommend MGSO, but there are some great mods to pick and choose from.
Tomorrowind: A hybrid list/guide that includes a lot of the classic Morrowind mods that live on MW Modding History or Fliggerty's.
So far the only issues I've had with my build are some minor typos. Everything works smoothly. Other mods I highly recommend: Weapon Rotate, the White Wolf of Lokken, Julan Ashlander Companion. Kateri's and Emma's mods use Westley's heads, so there are neck/body issues when playing with MacKom's heads. Lastly, I recommend using the lean version of Galsiah's Character Development. I've played with the original, and the lean version throws up far fewer errors--almost never. If you don't adjust your LO too much after starting a game, you won't have any problems.
The biggest issue is actually MacKom's Races Redone and missing neck textures with full-face helmets. The list of affected helmets is pretty small, but I'm a Blender/NifSkope newbie so it's taking me a while to get around to making a personal patch.
I think there would be real value in updating the STEP forum guide or creating a new one based off Neovalen's Skyrim template. There are a lot of poorly-packaged Morrowind mods, and without an xEdit tool it felt like going back to square one.