How about just making a game as you want to, instead of doing what others do? Making a game is like painting a picture; if you just follow someone's instructions line by line, it's really just their painting rather than yours.
but that's just the thing... How often have you seen a free-roam rpg??? Let alone one that was successful??? I mean, an adventure game, I can see a free-roam system, but an RPG? Where everything is based on stats only?
I mean, with free-roam, you can attack from afar and utilize maps in a way that you can avoid getting hurt by tougher enemies... But if you are in an RPG? You have no choice but to take a few hits in order to dish out a few hits, ya know? And that makes free-roam difficult...
basically, if you make the dungeons progress in difficulty, you would have to play them in order anyway, and it wouldn't be free-roam, and if you don't have them progress, then the rest would be too easy...
Eh...
In conclusion, I guess that B is ok if you use the script to have enemies level up in relation to character levels...