Here it goes.
First thing that comes to mind has already been mentioned; its a player focused game, where my skills often take priority over my character's skills. I don't exactly hate this, but it just feels very....wrong. I really don't think combat was as boring in Morrowind as people say it is. Sure, its no hack n' slash, but it doesn't need to be. Hell, I still find Daggerfall's combat fun. A few tweaks to Morrowind's combat like positioning, locational damage, greater elemental damage variation, the ability to use the environment to your advantage, and improved physics would be much better than Skyrim's system, in my opinion.
Secondly, and probably the most common complaint, is the quests. Morrowind's were not better. In fact, they were usually worse. Oblivion's were better. They took a step back in this area. Guild Quests are the worst offender. The Thieve's Guild aside, the questlines are short, terribly paced, and just all around lackluster.
Another big thing is aesthetics. TES games rely heavily on aesthetics. This is something completely subjective, and thus I can't provide an argument for it. I don't like the Nordic themes, even if it does fit lore.
Then there are all the things that were cut, i.e. a [censored]-ton of spells, mysticism, acrobatics, and athletics. Acrobatics and Athletics could have just been merged, and I see no reason for getting rid of mysticism. They didn't even give an in-game explanation for it.