Actually Masuda has explicitly said he's thinking of a way to tie up the Kalos and Hoenn saga. But who knows how he's gonna do it? Prolly with a Destiny Knot?
there's always the possibility that kalos is almost right next to the orre region separated by a mountain range.
hoenn seems to have some kind of commerce with with kalos
most of the pokemon in both orre region games where imported from johto & hoenn
all of the wild pokemon in orre can be found in the wild in kalos, except phanpy, wooper & sandshrew
it's possible that the wild phanpy, wooper & sanshrews might have always been in the area but not in that big of numbers til XD.
Colosseum happen soon after the events of R/S/E/OR/AS
over the course of the 5 years between Colosseum & XD the orre regions habitat became more filled with life
if orre is next to kalos, then its possible that the reason orre became a wasteland to begin with might have been the ultimate weapon & the use of mega stones rising caused their energies to spread to lands near kalos, especially if we use x's legendary over y's:
Legends say it can share eternal life. It slept for a thousand years in the form of a tree before its revival.
When the horns on its head shine in seven different colors, it is said to be sharing everlasting life.
there's a possibility to both ho-oh & xerneas might have some connection given that both of them have the power to bring back the dead, and are biased on eternal life & rainbows
so it might also be possible that ho-oh at at least a few times perched upon xerneas(tree form) and got pollen stuck to its wings that eventually was used to bring back the 3 legendary beasts to life
this might also mean ho-oh was vising the xerneas tree before heading over to the orre region & bearing witness to the events of Colosseum spreading xerneas pollen and giving the land new life & possibly reviving a few of the pokemon species that started showing up in the wild 5 years later
we can further speculate that the pollen got mixed with the sand & later got hit by the radiation triggering a territory change & revivals
if we exclude the first 3ed gen games counting them as a parallel universe, it's possible that both the orre region games are only connected to the hoenn in which looker washed up in with all the trading being done with cross-universe item trading.
taking into account the state of affairs in orre its possible that mega evolution could exist right next to the orre region without it becoming a topic of commonplace due to the odds of getting a pokemon there, let alone a mega stone & keystone
shadow pokemon might have been inspired by mega evolution to begin with.if cipher wanted to take over the world while knowing of the existence of pokemon to can mega evolve if the bonds are strong enough & if the trainer has both of the stones required, it would make sense for them to take the more mafia business stance on it & find a way to bring immense power in a pokemon without all the hassle & limitations.
add this all together and we got the possibility of orre being the connection between hoenn & kalos
then again there might be some underground region that lies right between hoenn & kalos that can only be accessed by two secret tunnels
1) hidden in the back of the sea spirits den
2)hidden underwater off the cost of everglade city
wouldn't that be interesting, a tri region squeal to both x/y & or/as with a long lost region in the middle.