Each character is a different hero (or villain). I don't think Random Hero 27 should be awarded the Flying Shark badge, when they never have visited the top of the Zig.
I enjoy the zone specific arcs too, but the one thing that is missing (may just be nostalgia getting me) is the travel between missions. Between base ports, ouro portals, mission transporter and the team transporter, there isn't a whole lot of travel going on.