These theories only cover the video games. Saying "Actually, in the anime..." has no power in this realm.
Dads in Pokemon are like assholes: Everyone's got one, and they all crush the spirits of their children with their continued and unexplained absence. The fact that almost every Pokemon trainer in the series lacks a father figure has long been the subject of speculation for fans. One of the most popular theories suggests that many of the world's adult males died in the great Pokemon War, an ambiguous conflict referenced by the gym leader Lt. Surge in Red/Blue. As with the majority of depressing fan theories, it implies unspoken amounts of death and destruction that doesn't line up with the tone of the source material. It's like saying that Aladdin takes place after the apocalypse, or that everyone in Calvin & Hobbes is an imaginary construct representing the people Calvin has killed.
There's a simpler explanation, and while it doesn't involve an insane deathtoll, it might be more tragic. See, there are some that think your in-game father is secretly this guy:
Remember him? He's the gym guide who miraculously appears at every stop of your journey. Did you ever wonder why this dude insists on stalking you every step of the way, offering you helpful advice and encouragement? If he truly was a professional gym guide, you'd think at some point he'd be required to help all the other unaccompanied minors battling for cockfighting supremacy. Maybe his tireless aid is a result of years of pent-up guilt after missing his kid's entire childhood.
That's the basis for a 4chan theory, which explains that the gym guide abandoned his wife when he learned she was pregnant with the boy who would grow up to be Red. A decade passes and the gym guide's conscience finally gets the better of him, and he dedicates himself to helping his long-lost son achieve his dreams. Though he's with Red every step of the way, the gym guide can't ever bring himself to admit his failures as a father to the one person it would matter most.
So yeah, you might know what kind of Pokemon you need in a rock-type gym, but check in with the guide anyway -- there's nothing he wants more.
There was always something... off about Weezing. Koffing seems to delight in being a puffy purple fart machine, but Weezing always seems like it's miserable and/or in unending pain. It can't be fun to have a second consciousness growing out of you, with what appears to be a third on the way. That nature would produce something doomed to a life of anguish seems strange -- but what if nature wasn't responsible for Koffing or Weezing in the first place?
To hear Reddit tell it, Koffing and Weezing were created by Team Rocket. Supposedly, they were trying to whip up a Ghost-type Pokemon by recreating their gaseous forms. In true Team Rocket fashion, they kinda half-assed it and we ended up with toxic balloons. I guess it's better than trying to make ghosts by murdering a bunch of drifters.
A couple key tenets support the artificial Koffing/Weezing theory. One is about where they're found -- in the Pokemon Mansion, which is an abandoned laboratory in the original games. They're not found anywhere else in Kanto, which could suggest they were created there and later invaded other regions, like that infectious Taylor Swift song that makes you sing it even though you don't know the words and don't like Taylor Swift.
The other piece of evidence is on Koffing itself; in particular, the skull and crossbones. It's the universal symbol for poison, but it's a human symbol. Which means that someone probably designed Koffing and Weezing with a warning label, and used the skull and crossbones after they couldn't find their roll of Mr. Yuk stickers. Even if you argued that Koffing itself inspired the poison symbol that people use, those bones appear to be human in origin. Either Koffing and Weezing were created in a lab, or they're the world's only pirate-type Pokemon.