Who will be the protagonists?
Brendan and May. They will be customizable, but they will be still Brendan and May. I know that Game Freak changed female character in HG/SS, but unlike Crystal, Ruby/Sapphire is not a third release.
What role will Wally play?
He will be your rival. He will also catch Ralts during capture tutorial. Except, he will appear more often than just... uh... twice. And he will have his own music theme. And he will have some small side story of his own. He will be most similar to Hugh, from existing rivals. I'm almost sure he will also have Mega Ring.
What roles do you think Juan, Wallace, and Steven will fill?
Juan will appear as Battle Frontier boss, Wallace will be Sootopolis Gym Leader, and Steven will be champion. I'm sure that they wouldn't want Juan to disappear (he was in B2W2, after all), but fans want Steven as a champion. Therefore, he will become Battle Frontier boss.
Edit: Recently, information about Steven Stone being interested in mega stones were released. I'm sure I noted that, but it appears I didn't. I mean, it's obvious that Steven Stone would interested in Mega Stones. Sometimes I forgot about obvious things... Still, I consider Steven to be champion, because I obviously knew about that, I just forgot about it while making the prediction (honestly).
Will there be any other League-related changes?
Roxanne will have Geodude and Nosepass. Geodude will have Rock Head as an ability. Nosepass will have Sturdy. Geodude will be level 13, and Nosepass level 16.
Brawly will have Machop, and Makuhita. Makuhita will be holding Sitrus Berry. His Makuhita will be level 20.
Wattson will have Voltorb and Magneton. SonicBoom will be replaced with Volt Switch. Magneton will have Mirror Shot instead of Shock Wave. The final Magneton will be level 25, and have Sitrus Berry. He will give TM with Volt Switch, and Thunderbolt after New Mauville quest.
Flannery's Torkoal will get White Herb, which will allow it to spam Overheat, and it will have rather arbitrary Flail replaced with Sunny Day. The mons will have higher levels.
Norman will get his own battle theme (see Korrina for prior art). First Norman's Slaking will be replaced with Spinda. Norman's Vigoroth will become Linoone. Slaking will hold Sitrus Berry. The Slaking will have Giga Impact (when you have Truant, recharge moves aren't any issue), instead of lol Focus Punch. He will also have more importance for the story. The mons will have higher levels.
Winona's Altaria will have Sitrus Berry. She won't have Pelipper anymore, because of X/Y three mons limit. The mons will also have higher levels.
Tate and Liza. Wow, this. I honestly hope they would not have just two very similar mons. Making predictions here is rather unsafe. They wouldn't remove them, and they wouldn't make this battle a single battle. But for a good double battle, they would have to have four mons. This is seventh gym, and while they didn't do it in X/Y, they will have four mons, to be exact, something similar to their Emerald team. The official format appears to be three Pokémon for singles, and four for doubles anyway.
Wallace. Yes, I assume the gym leader is Wallace, which isn't that obvious, considering Emerald's changes. Considering my previous risky assumption that previous gym leader should have four Pokémon. Honestly, they surely must have noticed the X/Y is too easy, so I'm going to assume Wallace will have four Pokémon (yes, it's a crazy prediction). Seriously, Champion has six Pokémon, so the player is better prepared for the final battle. Anyway, he won't have his Luvdisc, and all Water Pulses will be replaced with Scald (you may have noticed how many water TMs are in the game - two, to be exact - Scald is practically confirmed, because why Gym Leader would give Rain Dance, which most likely will be in Abandoned Ship instead). The levels will be increased.
The Elite Four won't change much, aside of level changes.
Champion Steven will have Mega Aggron, and slightly increased levels of everything. This also means the Aggron will be the final Pokémon, not the Metagross. However, the Metagross will be also highly leveled, which is normally property reserved for final Pokémon. Steven will also appear before Ever Grande City on few occasions (just like Lance, Cynthia or Alder), and will give Mega Ring once.
Will Scott make a return? If so, what as?
Yes, he will return, and have the same role as in Emerald. No real changes here. Oh, and I assume Battle Frontier to exist, I think that Game Freak doesn't want to risk not having it.
What will Rayquaza's role in the story be?
Well, considering sneak peek looking like the Rayquaza's cutscene from Emerald, I assume the Rayquaza will be needed to calm Kyogre and Groudon. But even considering that, it's still Ruby and Sapphire remake, not Emerald remake, you won't get to catch Rayquaza before defeating the Champion.
Assume Kyogre and Groudon receive Mega Evolutions. What do you think
— their types / abilities / signature moves will be?
— their roles in the games will be?
— of their Megastones being the Red/Blue Orbs? Or will they be something else?
First of all, their abilities. I assume they will be permanent version of Drizzle and Drought. Let me explain. You will battle the Mega Kyogre and Mega Groudon during the plot, in similar style to Black/White Kyurem in B2W2, during final battle with evil Team Magma/Aqua Boss (which is more evil than in Ruby/Sapphire). The legendary will be possible to capture post game. You won't be able to capture it. It would be anti-climatic if the sun or rain would end during the battle. The types will stay, they wouldn't want to confuse fans who played original Ruby and Sapphire.
Considering that Soul Dew is not a Mega Stone for Lati@s, I would assume Red and Blue Orbs aren't Mega Stones. That would get confusing, as the description would have to hide the fact it's Mega Stone, which could be too confusing after capturing Kyogre/Groudon. Instead, there will be two new items called Kyogrite, and Groudonite. You can guess what they do (hint: they mega evolve).
As for signature moves, they won't get any new signature moves. The original post mentioned them, but honestly, I'm almost sure they will want to make this compatible with X and Y.
But seriously, this question assumes they are mega evolutions. I honestly think that "Mega" Groudon, and "Mega" Kyogre aren't in fact Mega, but new formes (the "never before seen Pokémon" is the same terminology that was used for Kyurem's formes, and mega evolutions are too predictable), just like Kyurem Black and White. This would make them compatible with X and Y, without having to update the game. Forced updates for local trades is something I think Game Freak would prefer to avoid.
What will the Version Exclusive Pokemon be?
I'm going to mention entire evolution families, even if I mention just one here. It wouldn't make much sense otherwise, because you can breed or evolve. Also, for Lati@s, I ignore Southern Island event, which most likely will exist.
Omega Ruby: Seedot, Mawile, Zangoose, Solrock, Groudon, Ledyba, Slowpoke, Pinsir, Shieldon, Dialga, Latios, Buneary, Aron, Dratini
Alpha Sapphire: Lotad, Sableye, Seviper, Lunatone, Kyogre, Spinarak, Seel, Scyther, Cranidos, Palkia, Latias, Glameow, Electrike, Larvitar
Will Generation IV - VI Pokemon be available in the wild?
— If so, what Pokemon will be included/excluded?
Yes. Magnezone, Rhyperior, Gallade, Probopass, Budew, Roserade, Dusknoir, Chingling, and Froslass.
But seriously, they will appear, but only in post game, after defeating the Champion. Too many to count however, so I'm not going to give over half of Pokédex.
What new Mega Evolutions will be introduced?
Latios and Latias. Mega Blaziken will stay event-only.
Edit: I'm going to leave the original prediction, to not cheat. However, Mega Sceptile, Mega Swampert, and Mega Diancie were confirmed (I'm seriously surprised on Mega Diancie, but whatever), which opens the way for more Mega Evolutions (if those would be compatible with X and Y, then more would be too). So, the prediction is Ancient Rayquaza (if not in this game, then in Delta Emerald), Mega Latios, Mega Latias,
Edit #2: Ignoring starters (which are known), I predict Latios, Latias, Kecleon, Jynx. Plusle and Minun don't seem likely... actually no, I'm going to predict them too, because that's exactly crazy. So, Latios, Latias (XY hacks), Kecleon, Jynx (trademarks), Plusle and Minun (yes, I know, it's crazy, but it's funnier when the pair is more unbalanced).
Where will the stones for the new Mega Evolutions be hidden?
Southern Island. They will be held by event Latios and Latias.
Edit: The starters mega stones will be given by Steven Stone.
Edit #2: Jynx will be in Icefall Cave (or if Sevii Islands won't be in game, Shoal Cave). Kecleon will be in Scorched Slab, because it's not that it's used for anything real anyway (and it's close to their usual location). Sunny Day can be moved to the Department Store anyway. Plusle and Minun will be in New Mauville, and exact stone will depend on the version.
New areas to be introduced?
Sevii Islands, which will include many species of Pokémon which aren't in the Hoenn Pokédex. The Sevii Islands will be also expanded, and will have in particular the location to get Dialga, Palkia, and Giratina (Dialga and Palkia are version exclusive, and Giratina requires both Dialga and Palkia). Also, Mt. Ember will host Heatran, not Moltres. The team Rocket's HQ won't exist on the island, but you will see Team Aqua/Magma's HQ instead.
Friend Safari that will look exactly like in Pokémon X and Y because Game Freak is just lazy.
Ideas for post-game content?
Uh, Sevii Islands. I believe I mentioned all in new areas. Well, there is Battle Frontier, and Safari Zone will include new Pokémon. What more you need, you have Sevii Islands. And, uh, Gym Leader rematches.
