What does Dishonored do better then Skyrim?
Ignore the fact it's two completely different games because QUALITY is QUALITY despite it's flavor.

I'm gonna go out on a limb and say stealth.

Pretty much everything aside from soundtrack. Funny a more linear game, had a greater sense of freedom than a huge open world game.

Stealth duh.

Stealth, though they're completely different, and comparisons shouldn't really be made between the two.

Quality is quality.

If a game developer make stealth good for their game
while another developer make stealth just okay for their game.

Keyword, quality.
And if you do not agree, then your actually saying that whatever a developer creates is the best it could ever be for that game.
Then it wouldn't be needed to criticize games, ever, again.

Well, I've played Dishonored more recently than Skyrim, but I'd say player movement. When I was a Wood Elf archer/thief, I still felt like a normal person wearing some fur armor. I bet there are mods out there that amend this, but vanilla, it feels clunky. Obviously, though, Dishonored would win in this category. It's all about being able to zoom around the level/map and leap up and over things.