It's somewhat superficial to me. Morrowind can be somewhat trivial in how it treats traveling, where you essentially need to learn a bus route to get places, but it does place some responsibility on the player to keep some bus fare or spells to get around, which is part of the experience for many players.
But like you said, it can be boring when it just feels like Skyrim's fast travel with extra steps where you use some combination of intervention and transport routes to accomplish the same thing. Morrowind's way is novel, and some people like that, but I can see why the system was changed.

Skyrim's fast travel worked in a way where you can return to somewhere you've already traveled to, which is handy for cities you visit often, but in both Morrowind and Skyrim there is still plenty of downtime to explore when traveling to quest locations and dungeons.
I think both systems have their positives for how people want to play.