I think they'll include megas as I think it's safe to assume that Pokémon from all Gens will be included in ORAS (if the previous remakes are anything to go by). If they're including all Pokémon, why would they not include megas?
Part of me is thinking (and strongly hoping) that megas won't be included for a couple of reasons:
1: Mega Evolution is supposed to be linked to Kalos, not anywhere else. (Of course, it's always possible that they've added to the storyline so that megas have been discovered in Hoenn. That would be easier to do if ORAS were sequels, rather than remakes, but would still likely be easy enough to incorporate into the story.)
2: *Before I make this point, I want to say that I've not played X or Y (nor have I paid attention to many of the features) and have only seen a Let's Play on YouTube. Therefore, I could be way off base with this point.*
While there might have been a lot of new features added to X and Y, megas were the main selling point of those games. Obviously they'll want to maximize profits and therefore sell more of each of the games. By adding the main selling feature of X and Y to Gen 3 remakes, they're essentially casting the boat away from X and Y.
Gen 3 is likely the most popular gen thus far. Coupling that with the main selling point of a Gen 6 game, why would a lot of people bother getting X and Y?
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If megas are to be included, I certainly wouldn't want Jynx to get one.
I made a thread a while back saying that I'd like to see an evolution for Jynx. The main reason being that I always see Jynx as part of a trio with Magmar and Electabuzz. All 3 got a prevo in gen 2 but only Magmar and Electabuzz got the evo in Gen 4.
A lot of people (purely based on those who I've spoken to about a Jynx evo) seem to think that it won't get one because of the controversy Jynx's design caused back in the day. I personally don't think that's a reason for Gamefreak not to give it an evolution, considering they obviously learnt there lesson and were careful not to make the same mistake with Smoochum. I'd much more prefer an evolution for Jynx than a mega form.
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Now, onto Groudon and Kyogre.
The forms shown on the box art are clearly different but I don't think that they're mega evos.
Have a look at all current mega evolutions. Now have a look at the original look of those Pokémon. They've all changed considerably, as you'd expect considering they're unleashing the untapped potential.
I don't think that Gamefreak would suddenly change how much they design a mega evolution for 2 legendary Pokémon, which they'll also know people would get hyped about.
The only thing I can think of for different designs is that perhaps Groudon and Kyogre are exposed to something which can unleash more power into them. (Similar to mega evolution but not as visually extreme. (This is bearing in mind that I don't think mega evos will be included.) This power may have something to do with the orbs or maybe new objects which are related to Alpha and Omega.)
