There is no place he ever said this. This just sounds like your subjective interpretation of something he said, or you misremembering. He said no TV/Movie characters period. He didn't say anything about who might own the rights to them.
References to the pokemon anime are just that. References, and nothing else. Simple text trivia. It's a completely different story to have a character that didn't originate from a video game and hasn't been relevant in decades.
Although as noted, if he wasn't in a video game, he couldn't be eligible regardless. As I said above, who owns the rights does matter. If he's a 1st party character, then the only thing holding him back specifically is the video game part.
Relevancy is an entirely different point, which I couldn't agree with more. He's only slightly known at best, and unless Sakurai or Bandai-Namco(whoever is directing the latest game) actually says "1st/2nd party characters must originate in a video game", this actual argument point doesn't hold water anymore.
The person is right, though. He said no "Manga/Anime" characters specifically when talking about 3rd parties. He did say to only suggest someone who originated in a video game for the Smash Poll specifically. Brawl itself had different rules. R.O.B., for instance, is actually a toy first, and was put into a game second, but since he's 1st party, isn't bound by that rule. But considering he changed his mind for the Smash Poll, I don't think we can say for sure what the actual rules are for his character choices(or Bandai-Namco's, or both) for Smash Switch. I do entirely agree that Captain N has no chance, more because he(since the person didn't really actually give us evidence he's a 1st party character) has no video game appearances. If he's 1st party, nothing stops him from being a legit trophy. I also would love to see a video game starring him, but his series is also full of 3rd party characters, most notably, some of Konami's.
But yeah, I mostly agree with you, but things could change down the line.