I think a lot of the disagreements on the forum boil down to:
People who want to be told a good story don't like Skyrim's story because, frankly, there's not much to it; people who want to tell their own story are happy that there is one studio left that still lets you do that.
Yess.... and no.
It depends on what you mean by "tell your own story". Like any medium, there are limits on how we can tell the story. The first mission of the thieves guild, for example, seems better suited to being a dark brotherhood first quest (sneak in, eliminate the mercenaries that get in your way, murder the owner of Goldenglow, escape through the sewer) than the thieves guild. It's remarkable what a difference stabbing all the mercenaries makes in that quest. .
Meanwhile the first mission of the Mages Guild (Under Saarthal, I mean) could be completed really easily by any kind of character, there is nothing to differentiate it for a mage at all. Considering the theoretical lesson in the college and the overall deadliness of magic, it would have been quite possible for Bethesda to have engineered that quest so that you were forced into a magical duel with a lich, as an example. (Or rather, the son of Gaulder bombards Tolfdir with magic while he brings down the orb-shield, and it is left to you to shield Tolfdir with some kind of ward before you both finish Gaulderson off in whatever way you deem appropriate).
The thing is, if you left me to tell my own story, I could do so in a much more fluid way than I am able to do through a game, which puts limits on what can happen, puts limits on what it delivers, and all in all ends up with a "Jack of All Trades, Master of None, which isn't at all better than a Master of One" game..