Actually, no, Butterfree didn't die. It's a very big misconception due to Anime-elitists who claim that Animes are, due to Japanese origin, filled with blood, guts, sex, nudity, everything the American broadcasts would cringe at in terms of kids shows having it. In fact, someone on Serebiiforums dispelled that rumor a long time ago, and he's a master at Japanese. As soon as Dogasu publishes the Redone "Bye Bye Butterfree" comparison. You'll learn this completely, as well.
Still, yeah, Pidgeot and Primeape need to come back. I don't know if Butterfree would need to be brought back onto the main cast, but they could visit. Or heck, maybe they could've had Butterfree, it's mate, and maybe their kids be at Oak's place making a home there.