Skyrim > Witcher 3 in:
* Core combat mechanics: Skyrim's core combat mechanics felt smoother and less twitchy than Witcher's; it was simple but satisfying
* Class/skill variety: no contest here. In Skyrim, you had the choice of being a battle mage, a conjurer, a warrior 2h/1h+s/ranged, an assassin, a thief, a vampire, and all combinations thereof
* Xp system: killing monsters raised your skills. Raising your skills made you level. No wasted effort, and no division between main quest/side quest exp.
* Crafting: Skyrim's crafting was very intuitive. You were your own smith. The main bottlenecks for high quality gear were the premium ores and souls. No need to carry around a hundred random ingredients. Lots of cool effects
* Repair system: repairs suck, Skyrim made it easy and cheap, ergo Skyrim repair system > Witcher 3 repair system
* Henchmen: you don't have Henchmen in Witcher 3
* Player housing: you don't have player housing in Witcher 3
* Guild membership: you don't have guilds in Witcher 3
* Dragons & all the game mechanics connected to them, including Shouts
* Mods
Witcher 3 > Skyrim in:
* Setting: Skyrim's setting is the already overdone TES and outside of the whole Shouts lore, its world design not at all memorable; Witcher 3 is Sapowski's twist on European folktales - which is, sadly enough, minty fresh in this industry
* Main quest design: the main quest is rather important as a motivator, and Skyrim never bothered to make it all that motivating; Witcher 3 has an actual plot, and one that is fairly well done
* Side quest design: Skyrim side quests were, with only a few exceptions, generic and straight-forward; Witcher 3 quests normally has twists to them and are dramatically deeper
* Voice acting: Witcher 3 has excellent voice acting; Skyrim not so much
* Characterization: Witcher 3 has awesome characters that draw you into the world; Skyrim is a hodge-podge of generic NPCs who you don't give a damn about
* Cutscenes: Skyrim has very few cutscenes
All in all, I think Skyrim wins as an RPG, but Witcher 3 wins as a storyfag indulgement.