My main complaint is that there is nothing to do after you beat Dagoth Ur. Sure, there are plenty of quests left, but they are all very simple and dull. Also, just getting to Dagoth Ur was very simple... I bet I had only explored a quarter of the map. I think if you play the game very well, then beating it is way too easy... there should be an automatic difficulty adjuster. I think I was around level 15 when I beat the game. Also, enchanting makes weaps way too strong. With enchanting, I was able to create a "flying" ring and a "walk-on-water" ring. I guess that made it a little too easy for me, since I could fly all the way up Red Mountain. But it was still kinda neat hovering over the heads of the enemies and seeing all the architecture from above.
That's what I think I loved the most... the architecture. It was so varied and imaginative that I just fell in love with it.
I think when I forget the storyline enough, I'll start a new character and try to play through it again, maybe with some of the mods. Are there any good mods out recently besides the pack guar mod?