IMO

From functional perspective Markarths house is the best. It got plenty of storage, lots of bookcases, and everything is nice and compact, also access to smelter and forge across the town.

Whiterun one is a runner up. Mostly because you get a lot of merchants in whiterun. And the enchant station is a short hop away anyways. Storage not the best and no mannequins . Best for alchemy because of the alchemy bag on the alchemy table.

However, from role playing perspective Proundspire Manor is my main "public" residence. It is very pretty decorated, but not my main house.

Depends on what you want it for but I hope this helps.. My first house was in Whiterun, cosy, good for storing things but knew what I really wanted.

I saved up coin and bought the house in Markarth. I moved my HQ from Whiterun to Markarth, took a few trips to do this. My new house is very roomy, with room to move about.
Heaps of storage for different items.

Since I make full use making poitions and enchanting, I've found the right place. My new Housecarl is there but I haven't any use for him. I already have a companion/ follower.