This is me thinking out loud:
Advanced tools and scripted installs being available earlier in the games life.
Scripted installs with Bash/OBMM make it much easier to deal with a 1000 esp files.
Overhauls
This is a concept that really took off in Oblivion. The idea of these far-reaching almost essential mods that change many different aspects of the game. I think this mentality stems from the very real possibility that a larger number of people find it necessary to change more things in Oblivion than in Morrowind. So what we get here is a situation where if you want to make a mod you pretty much have to make it compatible with the popular overhauls or many people aren't going to play it. Thus massive compatibility folders were born.
What do you guys think? If you find this topic interesting I'd love a history lesson from the people who know about it. Like I said I'm pretty much an outsider.