Well for me when it comes to Morrowind vs Skyrim/Oblivion it's definitively about the atmosphere of the games.
Even though it plays like ass at times, I get way more immersed in Morrowind than the others. The world truly feels like a crapsack world that you'd want to save, and the main storyline is actually interesting.
Take the main villains for example. In Morrowind the main antagonist is driven by personal desire for power, with the world and his actions fueled and shaped by political intrigue. In both Oblivion and Skyrim on the other hand, you get the classic "For the Evulz!" villains, with both their roles as villains not really having any further explanation other than being self-evident ("the World-Eater" and "the Prince of Destruction" aren't really the kind of dudes you'd invite to your party).
Oblivion: Mr McGuffin dies, enabling "the Prince of Destruction" to go fuck shit up. Which he does because he's the prince of destruction.
Skyrim: The World-Eater awakens... To eat the world.
???Tes VI: Shit's fucked.???
...
Sure the game doesn't have fast travel which can be annoying, but that annoyance is imho an acceptable sacrifice for the complete rags-to riches gameplay and storyline experience that the game provides:
In Morrowind, when you start of you'll get molested by a couple of Mudcrabs, but at the end of it you'll be able to punch out a god. Oh, and jump over oceans (fast travel!). Early game Morrowind is much harder than IV/V, while the late game offers more mucking around and ridiculous stuff. Oblivion's leveling system was horrible, and Skyrim sure did fix that, but you're still playing handheld and on a leash.
I'm not saying that I think Morrowind is per se better then the later tes games; that would be a lie. But it does have it's merits, and if you haven't tried it I think you should! Oh, and bashing Oblivion aside; the Shivering Isles was awesome.