D/P stupidity makes me weep.
If there's a third Legendary (I have no opinions on this matter) to be the equivalent of a D/P Rayquaza, it will likely be Matter. Why? Because no matter who wants to argue the fact, this game is aimed at ten year olds, and the majority of ten-year-olds aren't going to grasp the concept of a 'Void' between universes. Matter will be more easily relatable to them and their educational level.
Though, I think it's all far too stretched. Perhaps this is just me, and the crappy Texas education system, bt when I was ten, my science classes involved the basics of weather and things like photosynthesis; as a Junior in high school now, Space, Time, and Matter are still blurry subjects we barely touch. Basics physics in my freshman year (Newton's laws and such), a little chem then and alot of chem now...that's the average HIGH SCHOOL STUDENTS education, and we're pushing this on fifth graders?
Then again, perhaps Game Freak is noticing that it's core consumer group is made up of 20-somethings who got sucked in during R/B/Y. Who knows, who cares.
And I'll point out, to assume we'll have a third box legendary is silly as hell. There is no patern when it comes to 'main' Pokemon, as has been demonstated:
R/B/G/Y: Charizard, Blastoise, Venasaur(?), Pikachu
This gen, unlike R/S/E, didn't wrap it's entire plot around three Legendaries, and was all the better for it. Notice that the starters are the ones on the box, earning them the title of 'main' Pokemon?
G/S/C: Ho-oh, Lugia, Suicune
This gen wrapped the legendaries into the plot a little more, but it still wasn't that noticeable. I think Crystal had the most legendary involvement, which consisted of you seeing Suicune here and there. I don't recall much about Gold, and never played Silver (which didn't matter, because they're sister games), but I can't remember having to do much with the legendaries to finish the game. It was mostly TR and their plot to forcibly evolve Pokemon.
R/S/E: Groudon, Kyogre, and Rayquaza
The first--and hopefully last--truly legendary based. You had to do everything swhort of actually catching the Legendaries to finish this ****ing game, and truly made Legendaries feel so unspecial, what with you seeing thwm every which way. With ten legendaries, eight of which you could catch in-game, it was total crap. Do you really want to see this again?
And, to whoever said that an uncatcheable legendary would no longer be a Pokemon, you're an idiot. The legendaries are supposed to balance things out, as we've seen in the anime and the game's Pokedexes. I would LOVE to see a legendary too powerful to catch, or too essential to natural balance to capture (as though Articuno, Zapdos, Moltres, Ho-Oh, Groudon, Kyogre, and Rayquaza weren't ****ing essential enough), that you simply got the Pokedex info for after extensive contact with the beast. It doesn't make it any less a Pokemon. It's data would have to be in the game anyway, so maybe one could battle with it, without owning it? All the the little whiners with a cheat device could appease themselves by hacking one.
Bah.