>>57378993In the WotC era, the changes roughly amounted to either adding non-holo versions of holo rares and/or adding in the small amount of cards from JP theme decks and premium files. Aquapolis and Skyridge were the only sets that were combined from 2 main sets each and those were the last sets WotC did before losing the license so that may have been a factor. The worst it got from them, besides skipping entire sets, was switching a few cards around between the two Gym sets for type variety.
JP sets were also easier to follow back then. Split versions didn't happen until Diamond and Pearl, special sets were actually special and not subsets in-between main sets, and the less said about the dozen rare rarities and sets that have set numbers of 360/190, the better.