Not necessarily. In Emerald is possible to obtain one of the Johto starters from Professor Birch, and if ORAS do like HGSS and borrow elements from the third version (aka, Emerald) then we may get the Johto starters with their Mega Stones at some point.
To be honest I still see megas as pretty unlikely. Birch gives them to you for completing the Hoenn dex. Which is essentially a post game accomplishment. For the last 2 games the regional dex accomplishment gets you an Oval Charm. Also part of getting them as a reward in Emerald was that there was basically no other was to get them (Besides trading from a gamecube) Where as now you can trade all three onto your game whenever.
Johto starters are hecka popular and I'm sure they'll get megas but I just don't see it happening in a "remake" game that isn't the next iteration of 2 gen remakes. My reasoning for this is based on three concepts that, I mean, are just GF patterns that no one holds them to, but just seem like they won't be broken:
1) The majority of mega stones are not obtainable until post game
2) You will only be getting gen 3 starters in ORAS pre-championship
3) the concept of a streamlined 1 mega or "playthrough mega" experience that is linked to starters
1 is just based on the fact that they seemed to want to streamline the "mega" experience in XY and make it so your team really only had one mega on it in playthrough, your second starter. It also makes all the cool new megas your reward for beating the game. Showing your friend your mega Tyranitar is proof of your awesomeness. Mega evolution is only for the best trainers after all. I deem it VERY likely the majority of mega stones will still be post game ORAS for the same reasons.
2 is based on the fact that they just never give out two sets of starters before you beat the game. The obvious exception being the most recent games however they did this because that way you get your streamlined mega experience. It lets them feed you your mega starter for the playthrough. Also, while the Hoenn dex is clearly gonna expand I just don't see them pumping that much non-Hoenn content onto your team during the playthough.
3 is just the side effect of 1. We might be able to find one or two other megas (or take our event Beldum for people who buy the game early) but really the game is designed so that you play through with your starter as your mega. The starters are the pokemon that are supposed to be "garanteed" to be on everyone's team in playthough. The ones everyone playing "bonds" with and grows to like. A huge part of why they're so popular. It just kind of makes sense that they will be your one mega as you become champion. So after gen 1 and 3 starters get to be your mega for a whole playthrough. It'll suck for gen 2 starters to end up as this sort of "tacked on" addition that doesn't get that much in game love and attention. I would full on expect gen 2 starters to be "playthrough megas" in a later game where we don't already have others.
That's just my take on how they seem to be treating megas for starters. but it's based on a 1 or 2 assumed "patterns" that so far has only happened in one game. lol, so it's not like it's THAT grounded. But it still makes sense to me. Trust me I WANT a Mega Meganium. But I just think game freak will give it to me to be my only mega on my team for an entire game playthrough like it seems they are doing with every other starter.