I have no issues with the lack of historical accuracy. The show has never been about keeping faithful to history, and that attitude rightly extended to Treasure Island. I think they were more concerned with telling an epic story, which they certainly did. What I really liked:
1) The final battle. Awesomely executed.
2) Rogers defeat. The way it paralleled his conquering of Blackbeard was masterful, and showcased just how dangerous the man really was. Since his first appearance, he was one genius against at least seven others, and he stretched all of them to their absolute limit.
3) Flint is the King, as far as combat was concerned. He destroyed Israel as easily as he defeated Billy.
4) Flint's end works far better than his ending in Treasure Island. IIRC, he drank himself to death, yet the character we were given could never fall into such a self-pitying end. Having the love of his life returned to him would be the only thing that could calm him.
5) Silver's ending was weak, and really undermined his character.
6) Roger's really should have won. If he'd ever acquired a partner half as competent and consistent as he was, the war would have been over in weeks.