Quick note: I still haven't finished TW3, so I'm avoiding spoilers for how that one turned out.
I think the Jedi are a better metaphor than I thought. New SW trilogy spoilers:
They could do the same thing with the Witchers. Jump far enough ahead that only two or three are left, living in secret, and maybe a few hidden books. The story could be about rediscovering the secrets and founding a new order that makes them less inhuman. Less the gruff loners to allow for more personality between them. They might even tweak the process to allow women to survive the mutations. It could include plenty of
'they did what with children?' moments. The result could be something akin to the way rat catchers were - respected member of society that did a job nobody else wanted. Or like sin-eaters (which is closer to the way they are now) - people who do something necessary for society, but aren't socially acceptable as a result (although the 'feared and hated' part could be toned down if they went that route.)
I could absolutely see a trilogy with each game standing alone, but with an overarching threat where you spend the games building up this new order of Witchers until you face it down - with all of your decisions weighing into the finale, ala Bioware (the concept reminds me a little of Inquisition - just done with more nuance and meaningfulness.)
What doesn't kill me makes me stranger.