I don't know the engine personally, but I could suggest something. That being that it's possible, and this is just a suggestion, but perhaps it has something to do with the elements? Like, all three are pure psychics, so there is no elemental advantage or disadvantage to speak for, and since Mew has the earliest hexadecimal location of the three, it defaults to our pink embryonic pokepal. Or perhaps because he's the final pokemon.

Actually, I think Bulbapedia has hacking info.

And learn what I learned kiddo. Not all hacks are possible. It'd be awesome to turn Contra into Halo. It's a little bit less likely than you think.

But no, those forums would be better suited for this question.

Given a few hours sleep, I'd like to add a thought to this conversation. That being that, unless you've got one hell of an idea, psychic pokemon are horrible to start off with. Not to mention, Mew? Boring as hell on one player mode. Great for fights, but no good actually fighting in the game. It's just weak sauce, you know? Like... I can see an Abra, a Ghastly and a Geodude. The problem is that with big monsters like Al, Mew and Mewtwo is that there isn't a challenge. You're running through the game, braining every creature in sight. Rival? Fuzz you, I have mew.

...

All in all, plot out what you're going to do. What will be most fun, not the easiest. If you could hack a cartridge and make Mew, Mewtwo and Alakazam the starters, go for it. No one will be impressed if you ROM hack the three strongest psys into the starter positions.