jpdx

The "regional" pitch seems to have run its course, as more and more regional Kit Kats are available outside their respective regions. Well stocked Donkis or the specialty store in the basement of Tokyo station or even some of the stores at NRT will have half a dozen+ boxes from faraway regions.

I think the most meaningful distinction for first timers trying to make sense of the Japanese Kit Kat scene is bagged vs boxed vs Chocolatory.

Bags are 300-500 yen; some will have standard Kit Kats, while others can be fancy flavors -- various green tea versions, raspberry, egg custard, sakura and soy bean, sake, and even the bake version (that's supposed to be heated in a toaster oven). Some of these are seasonal, but they're recurring and nothing "special." These can often also be found (often with a delay) in Japanese grocery stores abroad (e.g., Marukai or Uwajimaya's).

"Regional" boxes come with a dozen small Kit Kats for 800 yen. There are also some smaller boxes in some cases (5 pcs). These include fancy green tea flavors, strawberry, pudding, citrus, wasabi, cheesecake, hot pepper, apple, etc. There isn't much change over time, although some flavors have disappeared (including, lamentably, the best Kit Kat ever, Cinnamon, sold around Kyoto). There are also "airport" boxes, which are smaller (4 pcs, IIRC) and rumored to be local, but really aren't (currently melon and strawberry) as well as some fancy convenience store editions, e.g., the cranberry/almond Chololatory knockoff. These editions can then have a revival as bagged version.

Chocolatory sells very expensive small gift boxes -- single sticks (Kit Kat Sublime) for about 250 yen and gift boxes that range up to $30 with fruity flavors (strawberry, passion fruit, etc) and weird concoctions (strawberry maple, butter, pistachio grapefruit, etc.). I think the Chocolatory brand now aims at the gift giving market more than the regional kinds, and indeed Chocolatory product sees more frequent changes and occasionally sells out. Chocolatories used to be pretty rare (Ikebukuro and Tokyo station only), but I've now seen them in Osaka, Fukuoka, and Kyoto, and they're probably elsewhere, too.

There's no firewall between the respective kinds -- already mentioned, there's a convenience store special (and now bagged) "by Chocolatory," and there's a fancy gift box version of sake (shaped like a bottle) and a bagged version of sake. In some cases, you'll be able to taste a difference between the expensive and mass market kinds, but sometimes not. Note that the vast majority of specialty Kit Kats are white chocolate based; seems as though dark and milk chocolate are much harder to combine with the flavors on offer.