Yeah, I think I will do something like that, but I'll wait until I reach that point. It will probably take me a while to figure out how to do that, and I want to try and get a beta out first! ;)
Regarding the other legendaries, I'll be replacing Groudon with Lugia, and Rayquaza with Ho-oh. I'm not sure how I'll do the dogs yet, as i'm not putting most of kanto in the game... They'll probably be available on some of the 'mystery islands', and replace the 3 Regi's. But as I said, I won't be working on that part for a while yet!
Also, does anyone know how to edit the title screen?