I didn't play the first OP musou, but the second one had an original storyline where they went wherever the fuck. Some of the levels were loose, abridged versions of actual arcs (like Kingdom Hearts worlds). The third (and one I'm playing) has two story modes: a Dream Log, which you take a custom crew from island to island until you beat the super big bad boss at the end (like OnePiece: Grand Adventure's single-player, which was fun as fuck), and it also has the Legend Log, which follows the main series story. This one goes from Romance Dawn through Dressrosa. For some reason, it just skips Whiskey Peak, Little Garden, and Amazon Lilly. Basically, after the East Blue saga, they go to Drum Island, then Alabasta, Jaya, Skypeia. They also skip the Long Ring Long Land arc, but that's honestly to be expected. Then they go to all the major arcs. Fuck, Whitebeard War (or Paramount War or Summit War) takes two missions.
Now, I like the game, because it does a really good job of abridging the anime into something that still has the same feeling as the anime. Not a lot of anime games do that, and it's especially surprising for me considering that musou's are a genre I didn't particularly like until I played Pirate Warriors 2. PW3 is even better.
That said, I would like to see them make those three arcs (Long Ring Long Land is already covered in a cutscene, which is all you really need from it) into levels, if only for DLC.
All this game really makes me want to do is to get back into the manga and re-watch some anime arcs.