Practical Gameplay Theory
It could be because Mewtwo was obtainable in-game, where as Mew was only obtainable through an event, which no doubt people would miss out on. I'm not counting the Mew glitch, as it was not intentionally put in the game (as far as I'm aware).
Anyway, for those who didn't get the event, their pokedex would go:
This could be very confusing for someone trying to fill their pokedex. Mew wasn't required to have a 'full' poxedex, and was never seen during the game, so it would be an unexplained mystery. Switching the positions of Mew and Mewtwo would be an easy solution to fix this problem.
Pokemon Mythology Theory
Another theory is that Mew was thought to have been a legend, or a long-extinct Pokemon. Yes, some scientists cloned it, but as they were working for Team Rocket it is unlikely they would have shared their discovery with the world. However, Mewtwo escaped the lab and so was recorded. Once Mewtwo was documented, then possibly the story about Mew came out, and so Mew was also added to the pokedex, but after Mewtwo, even though it had to have been around before it.
Yes, I made up the theories and their names on the spot, but they are my best guesses both of why it made sense in terms of the game, but also how it could fit in with the Pokemon world.