One difference is Witcher 3 is made by a studio that doesn't have a huge following of haters. Nobody hates CDPR because they don't have a reason to, they haven't bought a popular franchise and forced it into something else. Skyrim was at a solid 8.5 user rating until Steam and Bethesda tried the paid mods trick, then Skyrim got a massive influx of 0's and in just 3 days it drops at 8.0, do you think the haters came back to change their vote after the paid mods idea failed? No, that's how accurate Metacritic user score is regarding the value of a game. I trust the journalist reviews more than an aggregate score of nobodies trolling and spamming and "getting revenge".
When the critic score is 1 point or 2 points apart from user score (like Skyrim was 94 vs 85) that's a sign of healthy evaluation, the arithmetic mean between those two is most likely fair. When the gap is 88 vs 46 then one of the two is very very wrong and the average doesn't work anymore, and in this case of Fallout 4 I think the critics are closer to the truth.