Because Mew wasn't intended to be one of the 150 pokemon you can acquire through normal gameplay. It was the "mystery" Pokemon, no one was supposed to know its existence. It was only attainable by
- Nintendo events
- Gameshark
- Game glitch
So yeah it makes no sense, but, if Mewtwo had been #151, your Pokedex in Red and Blue would have a gaping hole in it at #150.
Mew was considered extinct when the pokedexPokedex was made but. But as Mewtwo was alive and known, he was placed first. Then MewsLater, Mew's resurrection of his species in emeraldEmerald by a scientist meant they could now get his info for the pokedexPokedex. MewsMew's original form in the pokedexPokedex was actually just "???" Pokemon, who could learn any move.