Honestly this post is a good place to start.
http://www.pokecommunity.com/showpost.php?p=8505424&postcount=8
But, because I'm nice I looked through it and figured it out. All you need to use is a callasm 0x80C4EF9 and you can fly anywhere that you've already visited. :)
Code:
#dynamic 0x800000
#org @start
lock
faceplayer
msgbox @m1 MSG_KEEPOPEN
closeonkeypress
callasm 0x80C4EF9
waitstate
release
end
#org @m1
= I'm the Magical Flying Tree!\nLet's go!
Something like that will work. It brings up the flying map, lets you pick a city, and you fly there. I believe the first non-fainted Pokemon is shown using fly, though.
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What are you so afraid of?