Personally, I think it's best to complete all except the final Hamish mission with Arthur, and then pick it up with John as there's unique dialogue regarding Arthur with Hamish.

I like to do "He's British Of Course" as John, because he reminds me of West Dickens in RDR1, because he calls John "dear boy"

Arthur's diary entries for stranger missions are much better. Better drawings. I'll go for Arthur on all of them.