I still haven't finished either, but I got about 80 hours in Morrowind and 125 hours in Skyrim.
Up to now, I think both have their pros and cons.
So far I've completed the main story up until the fourth and fifth trials and I think it's superior to that of Skyrim's. The cultures and background stories of the Dunmer and Dwemer are also far more interesting than the tales of the Nords in my opinion.
The game suffers from being very slow though, especially in the beginning. Your character moves like a snail and everybody battle is annoying as hell since all your attacks keep missing. The random success system is bullshit in general if you ask me. It feels too much like dice rolling.
Lastly, everybody always praises the landscape of Morrowind. I do like the alien look of it, but I think a large part of island is quite cumbersome to explore (mainly referring to the Ashlands).
Way better than Morrowind in terms of gameplay. I like the level system a lot and the battles are far more fluent. The fast travel system is a plus to me and the quests are also better overall (quests in Morrowind had very little variety). Lastly, Skyrim has the best soundtrack in my opinion.
On the negative side: The main story seems so-so to me (I'm at Alduin's Bane quest). Also, the sidequests are a little disappointing. You'll blaze through most of them within an hour or three.
To be honest, Oblivion is actually my favourite Elder Scrolls game. The major sidequests were way better (especially the Mages Guild) and I think it had the nicest landscape to explore. The landscape was colourful, had a lot of variety and was easy to traverse.