I think both are inferior to Morrowind in a lot of ways: plot-line, multiple competitive factions for identical characters (ie. which House to join, whether as a magic user it was better to be Telvanni or Mages Guild, the only game of the three to have "church" factions for healer-classes), the creation of artificial-caps on magical skills (such as effectively reduced the value of alchemy as a skill (offset by the insane weight of alchemy equipment)), the missions were better. I don't necessarily want class or race balancing...it's not as important in a single-player-only game. All told, Morrowind was the best written of the three even if it had a comparatively-weak plot.
Sure Morrowind had its' shortcomings. Some have been addressed with mods (such as reskinning it to take advantage of advances in graphics and improvement of sound quality), some such as the absence of homes you can buy, fast travel and horses simply continue to be annoyances.
I really hoped when they came out with Skyrim that they were going to incorporate the best of Morrowind and Oblivion...but they seem to have doubled-down on everything they fucked up between them in attempts to appeal more to casual gamers.