Well... I guess a lot of people day-dream about pokemon being real. I do, quite a bit actually. I'd like a Pikachu, Dragonite and maybe a Char-mander/izard. Heh, I'm going a bit off-topic here...
But, if the Latis were around, remember it would be a ka-zillion times harder than on the games. Things would take longer (it doesn't take 5 seconds to fly, in real life), the land is actually bigger (since they make things bigger to save time, I guess...) and I don't think technology would be that up-to-date, like, the marking map or the PokeDex being able to track things...
Also, remember, that legendaries are also not as happy to accept you than they are than the movies/games. They have expectations, and Ash, being a Mary-Sue*, always gets his way. In the games, you are always practically a Mary-Sue, being the hero/heroine and all, always win.
I'm still guessing why pokemon are so ready to trust trainers that attack and capture a free them. Shouldn't they be angry that their freedom was taken away, and are now forced to fight? Latias, being a happy, care-free pokemon should love her freedom, eh? Being captured might put her into shock! I think, though, Latios might be sorta offended that someone might try to attack and capture him... Being a strong and (sorta) up himself pokemon (that's what I think...). Heh, but thanks to the fabulous idea of fiction, anything is possible.
Anyways, that's my two cents.
*If you don't know what a Mary-Sue is, it's a person who's pretty much perfect. Just think as a person who always wins his battles.