The same could've been said for the Hoenn games, since Rayquaza is in RS, and the Johto legends are available in the Kanto remakes, as were the Johto bird Duo through an event in addition to having the native legends (bird trio and Mewtwo), and Jirachi and Deoxys were event legends. Yet Emerald was still made...and Rayquaza didn't even gain a forme like Giratina. It main selling points were the two evil teams in one game, and the battle frontier... So maybe Z will have Flare want to control both Life and Death (that way better controlling the population), and have a new location.
On topic: It's a funny how Hoenn's only foreign legends in the originals (well Emerald as RS lacked foreign region legends) were all event mons (Mew and the Johto bird Duo), and now look at it's remakes. Johto has something similar too, as GSC lack Mewtwo and the Bird Duo, leaving the Kanto part devoid of legends to capture, only for HgSs to fix that (in addition to adding the Weather trio (Johto and Hoenn seem to have a remake exchange legend program going on xD...and the Sinnoh trio (well D and P as we still need confirmation on G) seems to tag along with the Johto mascots (well H and L, as we don't have confirmation on S yet) and Hoenn mascots ever since HgSs...actually these three trios haven't been available in any game since then).
