So, since I am still playing this in 2020...
I think leaving so many houses to choose from, the makers of the game did have in mind for us to use them. If you have a faible for decorating and roleplaying, it is possible to create a really sophisticated house. Rather like animal crossing. :) My favorite locations were:
1: Abandoned House (Aleroth, north) - It has a table to set, a bed, and a built-in storage box. Some prefer the one further to the right, because it has a cellar.
2: Shop (Aleroth, south) - It has a bookshelf, and, being a shop, a complete storage room. Not as much dust as the abandoned houses. I also set up a corner for kitty.
3: Jeremias Hut at the River (by the Cursed Abbey) - Very peaceful location with a haystack and cellar as hiding places. You find the only movable bed of the game here.
4: Bar (by the Dwarven Inn, lockpick it and chase the ghost out) - Everyone wants to own a bar, and there's free ale. I added the bed from Jeremias hut to the next room.
5: House of Timmy's Family (by the Archer Guild) - Finally real furniture and framed pictures, a kitchen and a tub of water outside.
6: House you can buy (Verdistis) - So far we have only been squatting; this is our very first properly owned house! (Don't leave anything there before buying, or stuff might disappear.)
7. Backpack (Sack of Wheat with Hay Bed inside) - I also like having a "backpack" with me for camping outside. Just put two bunches of hay inside a sack of wheat to create a hay bed in it (instruction: unravel one stack and then put the second bundle on it). To your own content, add a pillow and blanket (both with no weight), some food and a drinking mug. You can later create a lighter and more classy one from a book with a hidden compartment (found in the thief guild). Put in a bed, the rug from the con artist at the blue boar in, and a glass of chianti. :)
It would have been fun seeing screenshots of all of the suggestions so far, just to compare how others set up their base. :)
Drink Up Ye Cider. 
