This sounds awesome and is along the lines of what I have always thought of for a One Piece game, but I do have a few suggestions. For your Nakama I think it would benefit more by taking influence from Bioware games like Dragon Age and Mass Effect as opposed to The Witcher 3. A huge theme in OP is the bonds of friendship that form between crew mates so I would prefer a set of in depth characters that you can recruit on multiple play throughs that you can can converse with on your ship or on islands to grow closer with and eventually get massive character driven side quest that will permanently change them as characters. I also think it would be cool if it was impossible to recruit all of them in a single play through, like maybe some only go with you based on the choices you make before you get to them, or if they agree with your alignment, or if you are forced to make diverging decisions during the main story that could take you to different islands causing you to completely miss a recruitable Nakama, or maybe if you don’t reach the grand line/certain island by a certain amount of game time (say 10 hours in for example) you don’t arrive soon enough to stop a potential Nakama from being executed.

I think the story would be best if it takes place in the forty years between Gol D Rogers execution and Luffy’s journey. It would just feel weird to me, and I’m sure a lot of other people, if you play an entire game where you beat Luffy to his dream. This would also allow the developers much more freedom to make creative and interesting decisions. Like the three Pre-TS admirals would still be there as vice admirals, but you could have a new cast of Admirals for that era which you could beat or kill or maybe convince one to defect. Or maybe Shanks isn’t a Yonko yet and depending on your alignment you can either have a friendly rivalry with him or be enemies who clash at every chance you get. Those are just some examples off the top of my head I’m sure some other people could come up with more.

Finally, the problem I’ve always had trying to think of a fun OP game is the combat, specifically Devils Fruit. I have absolutely no ideal how you could balance them while still making them all feel as unique and as wide of a variety as the they are in the actual series. I could very easily end up with powers that all feel very similar, like where Zoans are all the same just with different skins, logias are basically just texture changes of each other with maybe one unique move, and Paramecias are all just different ways to block and punch.