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 Pokedex was made. But as Mewtwo was alive and known, he was placed first. Later, Mew's resurrection of his species in Emerald by a scientist meant they could now get his info for the Pokedex. Mew's original form in the Pokedex was actually just "???" Pokemon, who could learn any move.