I see what you mean about the abilities, although there is one thing about the Pixilate-variations that might discourage them from doing it. (well, on like 2 Pokemon anyway)
It wouldn't make sense for Lopunny or Audino (Audino wouldn't get a new ability but the same logic still applies) to, upon Mega Evolution, suddenly not be able to actually use their Normal type STAB.
But Sceptile could easily have used a Dragonify or something... hell, it learns plenty of Normal moves via TM, yet in X/Y it can only get Dragon Breath and Dragon Claw, with the former being an egg move and the latter a TM. (I'm expecting that, ala Ampharos, Dragon Pulse is added to its level up moves so it has a decent Dragon STAB)
However, there are 2 things that I believe are the most likely candidates for new abilities: Primal Groudon and Primal Kyogre.
(or rather, upgraded versions of Drought/Drizzle)
I think that now they have badass forms and are the gods of the weather, they'll reinforce that by giving them better sun/rain, especially since Drought/Drizzle are on a few regular Pokemon.
(although I can't help but have a sinking feeling that they'll just have perma weather abilities, when they could have something creative instead)
also, one thing that's definitely worth noting about Primal K/G:
On their page on the ORAS site, it says something along the lines of 'it appears that [Primal Groudon's] ability might get boosted'. This seems like a direct confirmation, no?
It also mentions to look forward to more details about Primal K's ability.
(unless they're just pulling a Zorua-evolution-method on us again)