Jigglypuff was one of the most commonly recurring characters in the Pokémon anime. It would often show up out of nowhere, use Sing to put everyone to sleep, get mad, draw on their faces, and leave; it was formulaic, but people liked it. However, the Baloon Pokémon's presence in the anime didn't last. Sometime during the Johto League, Jigglypuff began appearing less frequently. By the time Ash made it to Hoenn, Jigglypuff appeared once and wouldn't be seen again for years. This was a fairly popular character, so to see her phased out of the anime so unceremoniously is somewhat perplexing.
How Often Has Jigglypuff Appeared in the Anime?
Jigglypuff's relevance can be measured by the number of key appearances it made throughout different legs of Ash's journey. In the first season, Jigglypuff made a total of seven key appearances with a few cameo appearances here and there. In the second season, it only made two key appearances, though that can be justified by how relatively short this season was. However, throughout Ash's Johto League challenge, which comprised the third through the fifth season, Jigglypuff only made four key appearances. In other words, there was always a downward trend for the Baloon Pokémon even before its final appearance.
Jigglypuff made what seemed like its last major appearance in Advanced Generation Episode 39, "A Poké-BLOCK Party!." In this episode, Jigglypuff finally found the one audience member who could sit through its performance without being put to sleep by its singing-- Whismur. With its ability Soundproof, the Whisper Pokémon would continue to applaud Jigglypuff's performance even after everyone else fell asleep. Unfortunately for Jigglypuff, Whismur inevitably passed out from exhaustion, and her quest to find a captive audience was left open-ended.
Jigglypuff wouldn't appear again until Sun & Moon Episode 42, "Alola Kanto!." Of course, a lot of characters and elements from Kanto were making their comeback as Ash and his classmates were taking a field trip to the region. That said, Jigglypuff did end up following Ash back to Alola and made a few more appearances from there. This was all part of the anime's celebration of the Pokémon franchise's 20th anniversary, so it makes sense that Jigglypuff would be welcomed back like this. From here, Jigglypuff made one last cameo appearance in the final episode of Pokémon Journeys.
Why Did Jigglypuff Lose Relevance?
Jigglypuff might have been phased out due to a lack of popularity. Besides the frequent anime appearances, it had all sorts of merchandise, a full-length song, and appeared in advertisements alongside Pikachu. It even became a playable character in Super Smash Bros., a title it continues to hold with the game series' latest release. Unfortunately, if the character didn't sell enough merchandise, then nothing could be done about it.
Jigglypuff might have left the show almost altogether in the Advanced Generation series because of the intended nature of that anime. Seasons two through five of the anime were meant to be direct sequels to Ash's ongoing journey to be a Pokémon Master. Following that, the goal was to give Ash as fresh a start as possible; this is why Misty was replaced, why Ash's clothes were changed, and why all his Pokémon except Pikachu were left with Professor Oak among other things. This may have also been seen as the anime's chance to give the Balloon Pokémon some semblance of a proper send-off.
If Jigglypuff has a comeback, it will be small but meaningful. With the series moving away from even Ash in the future, fans of the Balloon Pokémon will be lucky if they get so much as a cameo. The infrequency of its appearances makes the few times it does show up nowadays all the more valuable.