Ghost Of Tsushima Ending EXPLAINED
2. No Matter Your Decision, Jin's Transformation Is Complete
Both paths lead to the same place. Jin is an outlaw, and he's lost his family. Of the two options presented, personally, I think the ending where Jin kills Shimura is much more impactful. Is it the right decision? Well, there's evidence to support both choices as being the "right" one. An argument could even be made that Jin letting Shimura go is a better way of conveying his adoption of the Ghost legend, as he's divesting from tradition and finding a different path.
Ultimately it boils down to what you think is the lesser of two evils. Do you abide by tradition and give Jin's adoptive father a peaceful end, or do you break with it completely with the caveat he'll be forced to hunt you for the rest of his days?
It's tricky, but while there are differences in each game's epilogue - namely the outfits Jin adopts and the type of weather the island defaults to - it's still the same result.
One would suspect that the night time, inclement weather that accompanies the "Shimura dies" ending is Sucker Punch's way of hinting that it wasn't necessarily the right path to take, but ultimately Jin still arrives at the same destination: an outlaw without his uncle, but with a different family and the people of Tsushima by his side.