If you think that the reason for Fallout 4 not winning the overall GOTY of the last 2 GOTY awards, is solely Witcher 3's story telling, I think you are wrong.
Yes, the Witcher 3 did a very good job at presenting its stories, and it has interesting, well written stories. But I don't think that a simple thing such as this is enough to earn a game an overall GOTY award. Perhaps best story telling award, but for overall GOTY, there needs to be something more than that.
I think the reason critics choose The Witcher 3 over Fallout 4 is because of the overall improvement of Witcher 3 in comparison to its predecessors.
If you look at the Witcher series as a whole, it is clear that with every new installment the newer games are largely improved from their predecessors, in all aspects.
The GUI is more easily navigated, the menus better designed, the combat less clunky and more fun, leveling and crafting more straight forward and easy to understand without losing their depth, character animations are better,the difficulty more balanced, side activities more developed and deep, monster amount bigger with the different creatures feeling unique and thought out regarding the place they inhabit, the ways they attack and behave...
Witcher 3 is improved on every single aspect over Witcher 2, and it did so while adding new mechanics and features, and without losing its character, without upsetting older fans of the series.
Now if you look at Fallout 4, while it is overall a good game, it didn't improved much over Fallout 3. Its graphics improved over it, but not as much as people expected, and it has some new features like weapon modding and the crafting / settlement building. Plus it has a a way better character creation system. But a lot of aspects of the game weren't really improved, and the way some aspects changed in Fallout 4 made some people even feel that Fallout 4 became worse on them instead of improving, like for example the dialogues. The characters still look like puppets instead of people. The controlls on PC are bad enough for people who generally prefer to play with keyboard and mouse to choose to play with a controller that one. Plus a number of changes like the reduction of dialogue options and ways quests can escalate, and to a lesser extent the lack of skills, make some people feel that Fallout 4 isn't Fallout enough. The technical problems of the game like frame drops and textures not loading up or popping-in way too slow in front of your face, doesn't help either.
So basically my suggestion to Bethesda is that instead of focusing on streamlining gameplay to catch a more casual audience, and just adding a few new stuff while leaving some other aspects of their games undeveloped or unimproved, to try to refine the core aspects of their games, aiming for overall improvement. Instead of cutting out skills completely from Fallout 4, they could instead improve on the way the skill system is presented to the player, like making a better GUI, and making a more comprehensive tutorial of how the system work. That way new players wouldn't be overwhelmed by it, and at the same time the older fans who liked skills wouldn't get upset. Because cutting game mechanics does not equal better gameplay.