Gym Leaders
Roxanne: Lv. 12 Geodude Lv. 12 Onix Lv. 15 Nosepass
Roxanne was a pretty solid first gym leader, however two Geodude is sort of repetitive, so if Onix happens to get in the games, I think it would be a good fit. If not Geodude is fine. In terms of the Gym design I think it needs to be changed to be on par with X & Y's first gym or Sinnoh's at the least.
Brawly: Lv. 19 Makuhita, Lv. 16 Meditite, Lv. 16 Machop
Not much to change here, the gym puzzle was pretty good and should stay the same.
Wattson: Lv. 20 Voltorb, Lv. 20 Chinchou, Lv. 22 Magneton Lv. 24 Manetric
I'd switch Electrike with Chinchou just to make Manetric more special and for added difficulty. The gym trainers can have that instead. The gym puzzle should definitely change. Maybe something more New Mauville 'ish'.
Flannery: Lv. 24 Slugma, Lv. 24 Houndou,r Lv. 26 Camperupt, Lv. 29 Torkoal
Switch Houndour with Numel for the same reason as before. The gym puzzle should stay the same as it was pretty solid, maybe a few extra chambers.
Norman: Lv. 27 Vigoroth, Lv. 31 Slaking, Lv. 27 Spinda, Lv. 29 Linoone
Not much to say here, again. The team is pretty solid and the difficulty is just right. They gym could be made a little more interesting, they need to match the grandeur of Kalos's.
Winona: Lv. 29 Swellow, Lv. 29 Tropius, Lv. 31 Skarmory, Lv. 30 Pellipper, Lv. 33 Altaria
The gym puzzle should definitely change. Something to incorporate heights a bit more. I found I ran throw Winona's team a lot easier than anyone else's and maybe adding a Swellow in would change that.
Liza & Tate: Lv. 42 Gallade, Lv. 42 Gardevoir, Lv. 41 Xatu, Lv. 41 Claydol
This was hard to change. Gallade and Gardevoir really fit them, but I'm keeping Xatu and Claydol over a lower leveled Lunatone and Solrock because of the EQ gimmick. I don't want them to lose their strength and I think this is a good way to keep it. The gym design should take Ruby and Sapphires, simply because it would look quite cool with X & Y s graphics.
Juan: Lv. 44 Mega-Gyarados, Lv. 42 Kingdra, Lv. 41 Wishcash, Lv. 41 Luvdisc
Another hard one to do, the 8th Gym Leader really needs a Mega this time around. Unless they make a Mega Kingdra, Mega Gyarados should do the trick, I made it so his old signature will still be apart of his team, but eliminated a 5th member due to Gyarados. The gym should reflect Sootopolis a bit more, and perhaps utilize dive.
Elite Four + Champion
The gyms should stay in a pre-set order with grand staircase's to the next member reflecting their team. The rooms should also be greatly improved.
All Elite Four should also have a mega.
Sidney: Lv. 47 Mega-Absol, Lv. 46 Shiftry, Lv. 46 Cacturne, Lv. 47 Cradaunt, Lv. 45 Mightyena
Not much too explain here, except obvious level changes for the inclusion of Mega-Absol.
Pheobe: Lv. 49 Mega-Banette, Lv. 48 Dusknoir, Lv. 46 Dusclops, Lv. 46 Sableye, Lv. 55 Mismagius
Obviously the repeats had to go, so I added Mega-Banette as her Mega, and Mismagius instead of the other Banette, as well as Dusknoir instead of a second Dusclops.
Glacia: Lv. 51 Mega-Abomnasnow*, Lv. 50 Walrein, Lv. 49 Froslass, Lv. 49 Mamoswine, Lv. 48 Sealeo
The queen of repeats lost her throne and now has a Froslass and Mamoswine instead. As well as a Mega-Abomnasnow, which I have no faith of being in ORAS but it's the only ice type mega, or heck, the only mega that could be put on her team without raising eyebrows. So until we get a Mega-Weavile or something, this will have to do, if the Elite Four members end up having Megas. I think the only thing stopping this is Glacia.
Drake: Lv. 51 Shelgon, Lv. 52 Flygon, Lv. 53 Altaria, Lv. 53 Kingdra, Lv. 54 Mega-Garchomp
Again, not many choices for a mega unless they add new ones. Other than that the only difference is small level changes and no Salamence.
Steven: Lv. 57 Mega-Aggron, Lv. 57 Metagross, Lv. 55 Cradily, Lv. 55 Armaldo, Lv. 54 Claydol
Mega-Aggron as the Mega, level changes, blah blah blah. He'll definitely be getting a Mega and if Metagross doesn't it will be Aggron.
Other Characters
Wallace He will probably be helping you along your quest and telling you all the lore about the weather trio.
Wally I don't want to do a whole team with him, but he probably won't get a Mega-Gardevoir as we just had Diantha, so his team will probably be similar.
Brendan/May If they stay the same as R/S/E no Mega Evolutions for the other starters. But if they become battable again, they probably will make Megas for Sceptile and Swampert, and they will have the respective Mega.