I get that they're 95% the exact same thing, but the devil's in the details. It's much harder to justify the kind of action you see in sci-fi in a fantasy setting, and it's much harder to justify the aesthetic character and mysteriousness of fantasy in a sci-fi setting.
Sure you can make analogues, like instead of a spaceship you have a boat or airship, instead of tanks you have siege engines, instead of scientists you have wizards, etc. But that can be such a tricky thing to pull off without feeling forced, like you're a fantasy author who really would rather be doing sci-fi, or vice versa.
It's especially apparent in video games. It just often seems like there are many more fast-paced science fiction games than fantasy games. At the other end of the spectrum, it also has the market overwhelmingly cornered in grand strategy kind of games like EVE Online, as well as in simulations like the 4X genre or the (thankfully) returning space sim genre, where fantasy seems to usually prefer somewhere in the middle with RTSs and RPGs. I'm not picky, but sometimes you really just want to make something explode, and sci-fi is much better at giving you that.
On the other hand, fantasy is much better at creating a feeling of mystery and curiosity, as well as with aesthetic variety. It also does drama a little better, in my opinion, because it has that mystery to back up the storytelling. For instance, it would be pretty difficult to work some of the environments you saw in Skyrim into a science fiction setting. Definitely not impossible, there's a lot of promise with upcoming titles like No Man's Sky, but it does seem rare.
So, for me the breakdown is:
Science fiction: immersion, action, scale, and detail.
Fantasy: storytelling, exploration, and variety.
I'll go with sci-fi, but only very slightly.