My only real gripe with quests and rewards is that it seems like you get the best rewards in the quest line, not at the end of it. Also a bit of an issue due to the smithing system (that Elven Shield is a lot less useful when you can just make one in a few seconds). Something that does need to be worked out, but not earth-shattering.
Nothing huge, but spoilering anyway:
Spoiler
Thieves' Guild: Nightingale Armor
Companions: Wuuthrad, Wolf Armor (Why? Because it's better than the Ancient Nord armor you can forge at the end of the quest line!)
etc
As far as the greetings and all, likely just a minor snafu in the files relating to status and greetings. Nothing worth getting a hernia over.
Quest length? Could be a bit longer, I suppose. They could always pad it out with the generic "go get this for me" and "go kill this guy" that was most of the Morrowind faction lines. I was fine with the Thieves' Guild here, while I felt the Companions could have done more. Haven't done DB yet.
Also fine with the loss of Attributes. I don't want to go into it here too much, but in an RPG attributes are meant to define a character and be pretty concrete - a high Strength, low Int character will never be much of a mage, if at all. In games where it's possible to raise attributes, to do so would require shifting focus away from his main role, quite possibly making him less of a warrior. In TES, there's no barrier at all other than "how much time do you have?". While people will try to defend it with "It made my character unique!" it's only at the beginning - most TES characters eventually branch out to be a jack of all trades type.
"Limiting the usefulness of skills". So without putting any real effort into it, I can't just became a master archer or an Archmage just because I like to shoot rats or throw my basic fire spell at a wall? Sounds like this adds a bit of character depth to me. My first character was a bit of a jack of all trades, pretty good at combat but not as effective because he tried to dabble as a mage. My second is a sneak thief - great when he's got the advantage, but hard pressed in open battle. Could you do this in the old system? Yes, but it makes it more concrete here - you can never be the absolute master of all skills.
Story and the game world: Fine with this. It makes you do a bit in the beginning, and the world has a general feel something is going on. People complained about Oblivion often not having anything to do with the story (since the world shattering Daedra invasion was a minor inconvenience at best aside from Kvatch), which is probably why Bethesda did it this way.