Winter Vacation '98
In what appears to be the last bit of fallout from the previous year’s hiatus, Pikachu’s Winter Vacation aired smack-bang in the middle of the Indigo League competition story arc.
It’s probable that had it been possible to follow the original schedule, the Indigo League would have already concluded by the Winter Holidays, and not ended up spanning the new year. Given this and lack of other significant markers, it seems to make sense to place these specials after that arc.
However, story progresses somewhat rapidly toward the Orange Islands once the league wraps up, and there’s not really a fitting place for these specials to live post-league without breaking that flow. Others have deigned to remedy this by placing them before the league starts instead, which works due to the lack of landmarks within them.
In the absense of a “better” or more concrete solution it makes sense to follow that line of reasoning. If you know of a better/more accurate one, please get in touch!
Source: GameFAQs Pokémon Message Board