Ho-Oh, Lugia, Entei, Raikou, Suicune, Celebi, Latias, Latios
Legendary Birds: while not catchable I could see a sub plot taking place in Kanto in which TR catches them which angers Lugia in HG and Ho_oh in SS and you need to free them and they fly off to Sinnoh.
Mewtwo: I could see the Berserk Gene becoming a key Item for it, and like Mewtwo only opens the cave up for you when you beat Red.
Mew: can be gotten from My Pokemon Ranch
Jirachi: Perhapses the event takes place in Mount Moon Square and you need a like say a wishing star and say like on Moonday night the
Clefairy are dancing and you have the wishing star you can use Rock smash to awaken Jirachi and then it fights you.
Deoxys: Birth Island
now here one why not thow in a Hetaran and have the story be that Blane was remolding his Gym when he found a Magma Rock, and awoke Heataran and Cinnabar's Volcano stated to erupt.
And also I would like to see contest added to HG and SS, and I would not mind if they charged it a bit to being two rounds of Appeals then a battle...
Also did any one like my Ideas on wild pokemon and trainer roosters, also the reason I gave Sage Li a Togetic is because we get a egg that hatches into a Togepi after we defeat Falkner
~Charles Legend