My speculation currently revolves around the names of the games and the nature of the conflict of the original Ruby and Sapphire, yet with more of the moral questions that the recent games have been in the habit of bringing up. Alpha Sapphire suggests a beginning (alpha being the first letter in the Greek alphabet) and many creation legends involving water. For example, the Japanese creation legend states that "In its earliest stages, for millions and millions of years, the earth may be said to have resembled oil floating, medusa-like, upon the face of the waters," [source:
http://public.wsu.edu/~brians/world_civ/worldcivreader/world_civ_reader_1/kojiki.html ]. Kyogre also has a striking resemblance to the description of the sea monster leviathan in the Old Testament, check out the Book of Job 41 for that (Groudon could also represent leviathan's counterpart, behemoth, depicted in Book of Job 40). Omega Ruby suggests an end or the latest of times (omega is the last letter of the Greek alphabet), alluding to, with the amount of science centers in Ruby and Sapphire, the vast amount of scientific developments and breakthroughs that humans have been responsible for in recent times as well as the concept that humans thrive on land (though, with technology, are very adept at traversing land and water as well as air, Rayquaza's domain, and space, Deoxys' domain). It should also be noted that both Legendary Pokemon reside in the Cave of Origin in the games and that the Regi trio defended the Tree of Beginning in Lucario and the Mystery of Mew.
Team Aqua and Team Magma each place a profound emphasis on a predominance of one of these elements, respective of their names. After the sea and land had been created by Kyogre and Groudon and Rayquaza came from the sky to quell the fighting, they went to rest in the harmony of the balance that the two had created, providing a place for Pokemon to evolve. Much later, some group of humans have some motivation to directly disrupt this balance between the water and earth, arguing the importance of one natural phenomenon over the other. These missions in direct conflict with the other disrupt the natural order and cause the reinstigation of the turbulence in which the planet began.
In consideration of the nature of these speculations and connections, I believe that the game's pivotal theme will be the price of progress and the social repercussions of all of human's behavior. Hoenn appears to respresent a Yin-Yang symbol, land filling one half and an active volcano in Mount Chimney representing the (as far as I'm aware) nameless spot, and the sea filling the other half and a dormant volcano in Sootopolis City representing the other nameless spot. This symbolism, that opposing forces cannot exist without the other, could have many modern social implications. In a region that introduced double battles, perhaps togetherness may be the solution to the upheaval of any taxing change to natural order. Sociologist Rene Maunier summarizes the concept of balance in progress well in his paper The Sociology of Colonies: "In aiming at progress--in the common interest, as always, of rulers and ruled--you must let no one suffer by too drastic a measure, nor pay too high a price in upheaval and devastation, for your innovation."
Who will be the protagonists?
May and Brandon, the original protagonists, will likely be returning in this game as the themed players. The blue and red coloration of their outfits, in addition to Wally's green hair, suggests to me that Wally may play a major role in this game. Triple battles between the three main protagonists and Kyogre, Groudon, and Rayquaza? A new green team that will teach us how to train a dragon? Obsession with the Ozone layer?
What role will Wally play?
Wally, with his bond with Gardevoir, will symbolize the connection between people and Pokemon. I believe many double battles, maybe triple battles, will revolve around his character.
What roles do you think Juan, Wallace, and Steven will fill?
Juan will be the Gym Leader of Sootopolis, and Wallace and Steven will have some very complimentary roles in the game. Steven Stone, with a capital S-T-O-N-E, seems like the kind of guy who would give the player a Mega Ring. I believe they may be alternating Elite Four leaders depending on the game version, or maybe they will battle against the player in a double battle. With Pokemon's apparent interest of advocating competitive battling through the revelation of EV mechanics, it may be natural progression that more double battles, like those done in the VGC, would be prevelant in the game.
Will there be any other League-related changes?
Perhaps with the new customizable trainer outfits in XY, the Coordinator competitions will place an emphasis on trainer style and advantages will be given to the player based on quality customization. Scott may also advocate the Battle Tents scattered around the region more, especially since they all rest in places where Pokemon Gyms are not established. As previously mentioned, I think there may be a great emphasis on double battles in gyms and the like.
Will Scott make a return? If so, what as?
Scott, as the head honcho of the Battle Frontier, will advocate players to join in actual real-life Pokemon tournaments by suggesting things like, "Hey this is a cool strategy. You should battle this way. Try that against your friends. I'm looking for the best of the best battlers," et cetera, et cetera, however direct he wants to be. Kinda like how people started caring more about EV training in XY, Alpha Sapphire and Omega Ruby might inspire players to battle in actual competitions more, and Scott seems like he'll get players to scoot to those new smaller tournaments that TPCi is starting soon.
What will Rayquaza's role in the story be?
To stop the fighting. Maybe there would be a team to tame Rayquaza and there will be triple battles with the player, the other gendered protagonist, and Wally. I think Rayquaza will have a role as significant as, if not more than, the one it had in Emerald.
Assume Kyogre and Groudon receive Mega Evolutions (dear Lord). What do you think
— their types / abilities / signature moves will be?
Alpha Sapphire, where the world began in darkness. Mega Kyogre would be Water/Dark type, and maybe its ability will be actual permanent rain to compensate for the new five turn Drizzle mechanic. A water type field move that favors water types would make sense, since a new mechanic in XY is those specialty field moves. Permanent rain and specialty field moves for a Mega Legendary Pokemon. Arceus have mercy.
Omega Ruby, where the world will end in fire. Mega Groudon would be Ground/Fire type, and its ability, like Mega Kyogre's, will be true permanent sun. A signature move that affects the field in favor of ground types, like those Fairy Garden or whatever they're called moves, would make sense as a new addition to be premiered by Groudon. Holy Surskit.
— their roles in the games will be?
To crush everything in their path. They'll cause really awkward weather patterns and fight against each other like in Emerald.
— of their Megastones being the Red/Blue Orbs? Or will they be something else?
It makes sense that the mega stones will be the Red and Blue orbs. It'll probably be that way.
What will the Version Exclusive Pokemon be?
Complimentary Pokemon, like Shelmet and Karrablast, Plusle and Minun, maybe even Pachirisu and Emolga, will be the general focus of the version exclusives.
Will Generation IV - VI Pokemon be available in the wild?
I think that some complimentary Pokemon like Shelmet and Karrablast will be introduced in the wild. I don't believe that many, if any, will be added before the main story is completed.
— If so, what Pokemon will be included/excluded?
See above for general speculation.
What new Mega Evolutions will be introduced?
Mega Castform, for the sake of weather; stone at the Weather Institute
Mega Zangoose and Mega Seviper, to emphasize the rivalry; version exclusive stones found near Fortree City for the nature style place or in the Aqua/Magma secret lairs to suggest the animosity
Mega Sharpedo, to match Mega Kyogre's type and for Archie's main Pokemon; stone found at or neat Sootopolis underwater
Mega Camerupt, to match Mega Groudon's type and for Maxie's main Pokemon; stone found at Mount Chimney
Mega Sableye, to match the version exclusive Mawile who got a mega evolution in XY; mega stone found in Mount Pyre if Mega Banette's stone is elsewhere. Perhaps those XY stones will be for sale at the Battle Frontier. Gotta push those competitive battlers
Mega Wailord and Mega Relicanth, to go along with their role to awaken legendary golems; stones will be in the tombs
Mega Salamence, because I think that dragon cave near Fortree would be a nice place to hide a mega stone in
Mega Exploud, because the Whismur cave seems like it would also be a nice place to hide a mega stone in
Mega Delcatty or Mega Milotic, because it may be a certain coordinator's favorite Pokemon, who knows with the Pokemon Contests coming back; stone will be found in that art museum in Lilycove
Mega Machamp, to compliment Gengar and Alakazam, I want to see more arms, and with the emphasis on balance, it could mimic those multiple armed deities; stone in Victory Road?
Mega Magnezone, because there's that Mauville power plant place; stone will be in the Power Plant
Mega Claydol, because it would be awesome and the desert is just asking for a mega stone; stone in the desert. Alternatively, it could be Mega Flygon
Mega Metagross???????, because Meteor Falls is just asking for a stone; stone in Meteor Falls
Mega ?????????, because Dewford Cave and Steven STONE; ervhjbshbkjc
Mega Walrein; because of Shoal Cave; stone at Shoal Cave
Maybe I'm dreaming, but Mega Smeargle would be really, really nice; stone at Artisan Cave
Mega Latias and Latios?, because Mirage Island?; stone at Mirage Island or getting to that other island will be plenty easier or will have to be like Mega Blaziken--event only
Where will the stones for the new Mega Evolutions be hidden?
See above
New areas to be introduced?
New areas, as in none that have ever been known before? None that would make sense. Maybe the Harmony Something-or-other at the center of the region, if I had to guess. Maybe secret bases will be more complex, and the evil teams may actually fulfill their goals and cause the sea to recede or the land to flood, and areas relevant to the new terrain will be created.
Ideas for post-game content?
Contests, contests, contests, and Scott wanting you to spend money at sanctioned Pokemon tournaments. A space-oriented quest would be absolutely wonderful, I had dreamed for one in the original Ruby and Sapphire with as of yet no fruition. Jirachi and Deoxys, take me to faraway lands. Looker missions would be really cool. It would be neat to dress up to match certain teams at certain times for sneaking around, especially with trainer customization as an option. Secret base exploration with PSS/Street Pass compatibility would be wonderful.
