Yeah, considering the Nintendo DSi's release, and the addition of legendary pokemon from the older versions, they do seem to be trying to phase the Gameboy games out. Much like including the legendary dogs into Fire Red and Leaf Green, and the birds into the Game Cube was an attempt to pahse the color out. So, you can probably bet we're going ot see alot of thrid generation legendary pokemon. Here's where I believe they are going to appear:
I also know not all of these will appear, but these are scenarios for if they did.
Groudon(SS): He will probably appear in another Terra Cave somewhere, at Lvl 70.
Kyogre(HG): Most likely in some sort of underwater Marine Cave, at Lvl. 70.
Latios and Latias: Roaming Kanto at Lvl. 45, most likley after you talk to Oak or Elm and they say somethign about rare pokemon being seen in kanto.
Asfor the legendary birds, I don't believe they will be featured, as they already are in Platnium, however if they are, does anyone rember the Orange Islands? Well, what if instead of the sevii Islands, they were to include the Orange Isles? One Island with quite a few towns and places to explore, possibly inhabited by Hoenn region pokemon, to replace the the Johto inhabited Sevii Islands. Along with three other islands that feature extensive caves filled with pokemon of the type of each respective bird, with each respective bird on top of each of their islands. This could be the nerve center for an event involving an event Lugia, like in the movie.
Celebi: An event in Ilex forest, where you go to the Apricot Pokeball maker, and he gives you the gS ball to take to the shrinne in Ilex, as an offering to the spirit of the forest. Celebi appears at Lvl. 30.
Suicune: A new lake is built into Ilex, like in the movie, and that woudl be where you find Suicune later on.
Entei: The burnt Tower of course, it would be made into more of a dungeon.
Riakou: I'll leave this one up to you guys.
-Lupe