Witcher 3 and Skyrim cannot be compared directly, because while they're both RPGs, they're hugely different in several ways.
Skyrim has a blank-state player character, in Witcher 3 you always play as Geralt.
Witcher 3 has way better writing, characters, graphics, dialogue system, and combat.
Skyrim has a lot more freedom when it comes to playstyle, and a lot more intricate world interaction system (hired thugs, random encounters, inheritance letters, etc.).
Witcher 3 is story-driven, and the story is its key point. Skyrim is more of a sandbox, where sure you can follow the story to unlock cool powers, but honestly the story itself is really boring once you've finished it for the first time. It's also really linear, and has no choices to make -- very much unlike Witcher 3, where choices matter a LOT.
Skyrim has a lot more options when it comes to modding, although I have to say I'm damn impressed with some of the mods I've seen for Witcher 3 despite the lack of a proper modding tool (the REDKit).
All in all, both games are, in my opinion, the best in their own categories. Comparing them to one another isn't fair, because of fundamental differences between the two.