Whiterun, being central to the entire game world, having 2x blacksmiths (great for buying up Iron ingots & ore for power leveling), Skyforge (Craft Nord hero crap) certainly has it's perks. It doesn't get it's own enchanting table (not sure if any houses do actually) which is a downside, and not a whole lot of storage containers... but enough to bulk organize crafting supplies, spare gear, etc. It's also the cheapest house. The most inconvenient thing about Breezehome is enchanting... you have to go ALL the way to Dragonreach castle to use the court mages table.
I don't know any of the other houses... but one with an enchanting table (possible?) and more storage wouldn't be amiss.
Secret rooms/basemants in any houses would be ideal for anyone playing a Necromancer archetype who needs a place to store bodies.
You also get rooms for guild questlines... though not houses per se.... The college in particular is a nice spot with decent storage, alchemy, and enchanting all readily available (available room right at the start is pretty weak... but a good free storage space. Upon completion of college quest you get a substantial room upgrade)
And why can't I have more than 1 waifu?? I should have 1 per house :celebration:
I think all the houses have an enchanting table, except for Breezehome. I'm not sure about the house in Markarth.
Hjerim has a secret room with both enchanting and alchemy inside it, that's really nice.
Haha, I'm sure someone will make a polygamy mod sooner or later. I'd fill my house with waifus if I could... :hubbahubba: