I find Markath and Whiterun just stupendously great. The houses architecture, the characters, the quests, the landscape around it... everything!
However, I think that Beth, probably, became a bit lazy in designing the other towns. Riften seems another copy of Bravil, Morthal, Dawnstar and Winterhold are just too small. Winterhold is so small that having a Jarl just seems stupid.
Second, considering beth is using medieval towns as inspiration for the game, I think people shouldn't have such big houses. In the medieval age there were buildings with more than 2 floors and each family flat was really small. In Skyrim, there is too much space between houses and they are too big for one family

There are a lot of parallels between real life and Tamriel that just aren't there.