>>56238121When the anime started, they were only planning to have it run for a year and a half until Gold and Silver came out. Then Gold and Silver got delayed, the Porygon Incident happened, and the anime just kind of sputtered on for a year in the Orange Islands to fill in the gap. Takeshi Shudo, the head writer, also got ill during the Orange Islands and early Johto, and he seems to have been the only one who cared about character arcs outside of the badge quest, so the lack of direction led to them spinning their wheels for three years. The ShoPro producer has also gone on record saying that his vision was for Pokemon to be like Doraemon, where things don't really "happen" and you can have characters last for decades at a time. So Johto was a 140 episode series based on a premise that was really meant for about 80 episodes (and even then, Kanto has quite a bit of filler in the middle), and the writing staff was mostly directionless, so they kept making one-offs that fit a formula rather than doing anything interesting.
BW seems to have been derailed due to the Fukushima catastrophe. The Team Rocket vs. Team Plasma storyline had an episode never air due to the earthquake, I think the plotline was just abandoned. That doesn't explain why Decolore happened and why the last third is a lot of nothing, other than I guess they were ready to start shilling megas and XY.