The Primary Inns in Skyrim are pretty good. Bannered Mare, Candlehearth, Winking Skeever, etc. I was just really disappointed with any Inn not associated with a main settlement, they're all exactly the same. Even though Oblivion's inns looked largely similar, they were often quite unique in both feel and internal Layout. From the doorless bedroll you can rent (And own) in Aleswell, to the isolated Gottshaw Inn between Anvil and Kvatch (My personal favorite), each Inn really had a unique feel to it.
Not so in Skyrim... sadly.
Aside from the obvious atmospheric and aesthetic issues I have with most of the Inns in Skyrim, they also lacked a good opportunity for content generation. Bounties are all well and good (Would be better if you didn't have to collect at the capital), but surely they could have come up with more radiant content to make inns a focal point of unaffiliated content.