Skyrim:
Game is too easy if exploiting smithing and enchanting
Marriage is shallow and not all can marry
Dragons can become kind of annoying after fighting a lot
Monsters are leveled to a degree
Companion AI can be weak at times
Quests are pretty linear
UI svcks on PC
Main storyline is pretty short
Mountains have some invisible barriers
Most dungeons are pretty linear
Map markers exist for most quests
Radiant Story quests are kind of bland
Civil war storyline is kind of weak
Some minor floating bugs and texture issues for a few when installing game
Morrowind:
Terrible textures
Terrible animations
No NPC schedules
Copy/pasted dialogue on about 90% of NPCs
Annyoing as hell cliff racers
Few quests
Boring quests
Linear quests
Terrible combat
Bad magic effects
No built-in house ownership
No werewolves or lycanthropy
No marriage
No real mountains
Bad level scaling, game becomes simple after level 15
Powergaming exploits all over
No birds
No fish
No mounts
No snow or any dynamic weather effects
No dynamic speed tree technology
No dragons
Extremely simple NPC/monster AI
Small amount of books/notes
LOTS of identical looking external towns and villages (same textures, etc)
No dynamic traps
No companions
Small world
No radiant story quests
No radiant AI
No civil war story feature
Main story-line is pretty boring and can be super short if desired
UI svcks on consoles and is cluttered on PC
Lots of bugs, broken quests
Dungeons are static with lots of reused textures and conventions
A hold-your-hand journal with all the details given which can't be disabled
Some location markers appear on map after talking to NPCs which can't be disabled
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I just have to say, those people complaining about Skyrim's new and innovative features never even had such features, period, in Morrowind. They may not be 100% fleshed out and working perfectly, but that doesn't warrant the angry level of complaints against them. When I eat at a buffet with only meatloaf, I don't complain when sirloin steak, turkey and ham is brought out even if it is a little rare, dry, or unsalted. I greatly appreciate that I have them in the first place.
Other than the free-form skill system and simplified weapon categories, I believe vanilla Skyrim is better in every way over vanilla Morrowind. Even WITH all the expansions, fixes and mods for Morrowind, I still think Skyrim edges it (barely). With upcoming mods, fixes, DLC and expansions for Skyrim, I believe it will beat Morrowind in every possible way.