Putting witcher 3 below FO4 is kind of unfair considering that the former shits all over the later in every single area. especially considering that it just won GOTY and FO4 didn't win anything except Todd Howard being the king of lies. Heck, I'd put TW3 and GTAV PC ahead of FO4.
anyways, i'd say my favorite games this year were witcher 3, splatoon and DB xenoverse.
I think the combat of Fallout 4 is much better than in Witcher 3 although W3 also has really good compared for an open world RPG. Also Fallout 4 offers much better exploration, better more interesting and diverse world. I also didnt like the story of W3 THAT much and the pacing was a bit off, but F4's story is obviously much much worse.
I also didnt liked the leveling system in W3, it has some nice ideas though.
And that W3 won GOTY is good for W3. "The Game Awards" by Geoff Keighley are nice, but they are not the official group that says which game is good and which game is bad. Also I can understand why so many people love W3 and I think CD Projekt Red is definitly the most impressive developer of this year.
Well for one TW3 is a medieval fantasy action RPG and Fallout 4 is an open world FPS with some RPG elements. Comparing the combat is like comparing apples and oranges.
FO4 removed so many things like skills, the dialogue system is absolutely pathetic, the voice acting is terrible, the writing is awful, quest system is like FO3/Oblivion/Skyrim with repetitive fetch quest and collectathon open world. The game engines graphics still look like something out of 2007, there is no excuse for a AAA game to look this ugly in 2015.
Also one of things that TW3 has is a diverse world: Skellige is snowy/mountainous, Velen has this spooky slavic atmosphere and Redania is like medieval London. Its atmosphere is one of the strong suits of the game.