It is not a HUGE problem, but imagine if Barack Obama gave you a secret box to deliver to the pentagon moments before he was assassinated and it took six months for you to do it. [censored] saving the world I want to go join the Thieves Guild instead.
Well, technically the President would already be dead, and your task would be to find a suitable replacement because the Vice President was in a coma or something. And the Russians were about to nuke us into oblivion. Tee-hee.
Anyhoo, this could easily be applied to Morrowind as well. Dagoth Ur is just as much of an urgent threat as Mehrunes Dagon, it just doesn't
feel that way because when you first travel from Balmora to Ald'ruhn, the place isn't getting tore up by Ascended Sleepers. The worst old Loincloth Man comes up with or without your progress in the MQ is the Blight, which isn't that bad if you don't go inside the Ghostfence.
The Morrowind MQ is much easier to ignore, but the only real reason for that is the limitations inherent to Morrowind-era technology. If Skyrim had been the the third ES game, and Morrowind was up next, I'm certain it would be a very, very different game from the one we know. The Imperial Legion would be clashing with Ash monsters all over the place, an avatar of Dagoth Ur would appear before you out of nowhere to deliver his messages more personally, Tel Fyr would be on an island floating in mid-air instead of on water, when you battle the nigh-nekkid one he sits on Akulakhan's shoulder and has it try to squash you like a bug, all kinds of crazy stuff.
Come to think of it, I really wish Morrowind was the next game instead of Skyrim, because all of that just be so amazingly epic.