Not sure if this count as unpopular opinions.
But I just don't buy into the theory "Game Freak wants people to forget about Jynx"
1. Porygon is way more controversial than Jynx is, from a Japanese point of view. It actually caused more than 700 children to end up in hospital!! However, as we all know by now, Porygon had received new evos TWICE.
Although it may not appear in the anime, receiving evos is not related to anime controversies.
2. Junichi Masuda keeps retweeting tweets about Jynx. Junichi Masuda nearly retweets all Jynx tweets that are sent to him.
This is primarily achieved by Jynx Club's twitter and club admin SeafoamIslander (known as j2y8n2x on twitter).
3. Jynx is officially shown to be the favorite Pokemon of one of the 9 core members of Game Freak.
This is seen from Game Freak's Japanese exclusive Facebook page, year 2016. (written in Japanese)
4. Jynx had been appearing in many Pokemon Center merchandise during 2014-2015. Most notably, the very advertised Pokemon Spooky Party series.
5. Jynx also appeared in many other Pokemon merchandise during 2014-2015. She was heavily advertised during the TCG release of Rising Fists/ Furious Fists. Jynx was in the TV commercial, card sleeves, and the card file.
A few months later, Jynx also appeared on an official card mat, unrelated to Rising Fists.
6. Pokenchi, previously known as Pokemon Sunday, a Japanese TV show, showcased an edited version of Holiday Hi-Jynx in 2012, with all the Jynx repainted into purple.
In 2016, Pokenchi celebrities were shown to have baked a Jynx pancake.
7. Jynx (black faced) appeared in the Champion room in 2012, episode 4 of Pokemon The Origin.