Tell Me I'm A Screwed Up Mess
I'd prefer the Villa / House option simply because you could get to it easier than a Secret Base located on some route somewhere. With the Villa / House you can just use Fly and get to it immediately and take care of whatever you wanted to. I did like the Secret Bases though.
If they do reintroduce a Secret Base or House option though I'd like to see a bit more customization. Not just in terms of furniture, but layout and design (of the flooring / walls / outside of the house or secret base). I remember what I found particularly annoying about RSE's secret bases was the fact that the layout of the floor was set in stone depending on where you made the base. So the whole "pick your location" type thing wasn't really relevant. I just went for the best floor plan.