The worst decision in pokemon history was the decision to remake Red and Blue after only the third generation.
It is the start of the downfall of pokemon.

It split work between two games now, The remake and the new gen. Leading to eventually putting out shit versions of both (ORAS and XY)
Led to the death of the superior third version of games. reminder that Yellow and Crystal were drastically different stories than RB or GS and Emerald and Platinum were essentially exactly the same as their base games.
and Then We dropped third versions all together for straight up sequels. And while BW2 were very different, USUM were pretty much exactly the same.
And worst of all it catered to Genwunners. giving us no reason to care about new pokemon, since they'll just keep re-releasing KANTOOO. every few years. Giving game freak no real insentive to come up with more then just a handful of good pokemon every gen.

The culmination of this shit reached it's peak in Gen 6 with the two worst games of the series releasing, and the pokemon games have slowly been improving since, but really we never recovered from the mistake that was FRLG