I agree with you, excent for Breezehome, I like Whiterun and the people there, the town is small but everything is centralized, very convinent compare to other town. The house style is easy and homie (if you know what I mean), it's not protentious like Markarth.
Yes, it's a shame that it does not have an enchanting table, I wonder what gives the designers this idea.
God only knows - maybe they thought since it was a "starter home" it didn't deserve an enchanting table.

It's still my favorite of the bunch, though, especially since I got a mod that adds some more storage items and the enchanter to it. It has the best location of all the player ownable homes, it's close to the front gate, and the complete smithing set-up right next door is a huge plus.
The house in Riften is a close second, but it doesn't have a convenient smelter nearby, and Riften is tucked way off into a remote and inconvenient corner of the map.
I completely agree with the post above about Windhelm, and I'd add Markarth as well. They're both just dark, dirty and depressing.
Proudspire Manor just pisses me off. Come on, I spent almost 40,000 gold to buy this place and all of its upgrades; how damned hard would it have been to code a couple of knapsacks and/or satchels right next to the alchemy lab and the enchanter, instead of making me store my things in barrels in another room which may reset after a certain number of days go by?

Bethesda just does a crappy job with player-owned homes in general. The house in Megaton (Fallout 3) was a total dump with lousy storage options. The one in Tenpenny Tower was a bit nicer, but it also had no storage and you had to go through a zillion loading screens just to get inside. Same with the Lucky 38 casino suite in New Vegas.
You'd think they'd know how to design a decent, convenient, pleasant-to-use player home by now.