Foreign Legendaries

>The Kami trio

>You chat with some kid from "A land far away" and he tells you about some cloud like Pokemon, the Kami trio are then roaming
>You get the Reverse Mirror from a Team Aero grunt post game when showing them to him

Writeen by meta:

Regigigas and new desert area:

Frontier Brain Brandon modeled his pyramid off a rumored structured in the desert above Mauville. Recently the desert has begin to open up and reveal structures, namely a pyramid. In this new area you can find yamasks and Cofagrigas, Siglyphs and Unkown, as well as other new mons that a need home in Hoenn.

Researches have reached an impasse in the new area and theorize that it is the home of Regigigas himself and that each of the Regi trio is needed to gain further entry. Capturing them and bringing them to a room in the pyramid allows you to catch Regigigas, who could possess an alternate form, like a Hoenn or Home form.

Ho-oh and Lugia:

After defeating all three teams, Maxie of Team Magma tips you off to a creature that idealized both Magma's and Aeros' goals/themes, a sky-dwelling fire Phoenix, Ho-oh.

In a previously inaccessible area of a Team Aeros dungeon, possibly in the sky, you find means to travel to an area in the sky where you can encounter Ho-oh. Possibly in the plumes of smoke way above Mt. Chimney.

Team Aqua grunts mention throughout the story a beast who also has claim to the sea and tides, Lugia, but the team's leader passed it off as inferior to Kyogre. Team Aqua occupied a seafloor cavern filled with whirlpools as their base of operations but were expunged due to unpredictable waters in the cave. This was home to Lugia until it was disturbed by the team. After the team halts their plans Lugia can be found in their abandoned, previously unseen base.

Lugia and Ho-oh might have traveled to the region when disputes over the land/sea/sky began.

Shaymin and Mew:

Shaymin can be found on Mirage island, which either still appears randomly or is triggered by an event. Possibly a sidequest/fetch quest requires you to obtain a gracidae flower for a couple and as a reward you're told the Shaymin legend. You can then speak to the professor and proceed to travel to Mirage Island.

Mew remains on Faraway Island. He is accessible upon completing the Kanto pokedex and inquiring as to what the missing number in the dex is. The professor gives you an old keepsake of theirs, a map to the uncharted island where a mew is rumored to be.

Palkia and Dialga:

The space theme of Meteor falls feels perfect for the Space beast Palkia.

Perhaps Palkia's lustrous orb can be uncovered here, were he can simply be recovered via fossil regeneration. Dialga's adamant orb can found the same way here.

Upon restoration of their fossil orbs, a scientist informs you that process was working fine, and the pokemon were amazingly the Sinnoh duo, but suddenly died near the end of the process.

If you take their orbs to Mt. Pyre to honor them you will be approached by the existing duo. After a difficult double battle with them they will give you their blessing and allow for their protege to be born. Later, they will replace Dialga and Palkia as the keepers of time and space.