Having been a long standing fan of both the Fallout and TES games, I found Skyrim to be a fantastic edition. I don't think there is a game that doesn't have its weaknesses, and any and all complaints about Skyrim's issues are valid. I think what it comes down to is; do the things Skyrim does right out-weigh the things it gets wrong? For me, that answer is a very easy yes.
The combat system takes a lot of lumps, but I'm not sure why. I know some find it rather clunky to sword-fight in first person, but I'll take that clunkiness over the combat systems of most any other RPG in a heartbeat.
As for the main story being a let down, I wouldn't know, as I have over 700 hours in the game (On one and only one character) and have yet to do much of it. Like someone else mentioned, it would feel hollow saving the world from the big bad dragons and then going back to being a traveling potions salesman. I do advance the main story, but only when I run out of other things to do, which is not often.
It can be a buggy mess at times, but having the power of the console commands has saved me many a quest breaking bug. I realize the "you can fix it yourself" thing isn't exactly a great answer to "this is the 14th broken quest I've tried to do", but at least it is do-able, and on top of that, the console can help you do lots of other interesting things that help you experience the game the way you want to.
Lastly, I often see the argument that the world feels hollow because you have no real effect on it, and this I can totally get behind. I wish they would, and will, make the world far more dynamic with the next installment.
I think all of these complaints though, when put together, don't faze me much simply because I don't see anything else that does this sort of game-play better, except for perhaps New Vegas. I'd call Skyrim a great game. The parts it does do right it does really right, and the things it does wrong, well, I have the power to change many of them. I can't say the same for nearly any other game. I suppose there is a reason it is my second most-played game of all time on Steam.