I'd say that the first version makes more sense. Yes it would take longer to set up, but having two giant posts seems very messy. Maybe group the Routes? #1 to #14, #15 to #28, and so on. Posts for "other Kanto locations" and "other Johto locations" to catch caves and such if you don't want to add each of them individually. And a "general" post, for stuff that crosses the regions: plants and constellations and stuff like that.