Well, I've always preferred Mewtwo to Mew (and Blissey. Have I mentioned that Blissey is awesome? You should make the giant ultimate super-awesome Blissey that-)ahem, erm, where was I...
Yeah, Mew would be great, but where would you put him? Also, I've heard that if you catch Mew in the wild, he doesn't obey you...
You should have the Professor give Mew to you if you complete the regional dex (though that might get a little complicated to script, since you'd have to somehow seperate the Pokemon you include in your dex from those in the National and Kanto dexes). Or maybe you could stick Mew in that cave where you caught the Cyndaquil, for when you come back and revisit. Or maybe you could rescue it from team Knox.
There I go again. Well, where do you think you'll put Mew, if you include him?
Oooooh, I just had a thought. You should stick him under a truck somewhere for nostalgia's sake! :)
Ah well, keep up the good work! I'm looking forward eagerly to the next release.
EDIT: I just read through my own post and noticed how incredibly goofy it was... sorry about that.