Usually we follow the listing in the country of origin. Had we done that for Pokemon, we would probably have 9 seasons now. I say probably only because it's the past and not because I'm not sure about our rule on the country of origin (just clarifying.)
But we didn't. I believe that for Pokemon specifically, it was separated by leagues and following the American format.
At some point, we have adjusted back to the Japanese format, hence why S&M is one whole block (just as it is on the Japanese website now) for example.
I personally think that to satisfy everyone Pokemon would need a Japanese and an American order, but the new site only supports one alternate order for now, and we are forced to select Japanese between the two.
It's a bit of a difficult situation, but I am of the opinion that we should rework the ordering separately from the chimera we have now in a clean way.
However we can't touch what we have now because alterations will definitely cause chaos down the line for every user. Please understand this crucial point, as it's essentially for your benefit (and everyone else's.)
The web archive is just there to show that there's a historical precedent to the ordering method that has been kept mostly consistently through the various versions of the official Pokemon Japanese website.