That's not all: as suspected, Groudon and Kyogre will have new forms in the new Pokémon remakes, Omega Ruby & Alpha Sapphire.
The information comes from CoroCoro magazine scans posted by Pokemon website Serebii. According to Serebii, Mega Sceptile (aka Treecko's mega) is a Grass/Dragon type Pokemon and will have the "Lightning Rod" ability. Mega Swampert (aka Mudkip's mega) will retain his typing, but will have the "Swift Swim" ability.
Groudon and Kyogre's mega evolutions, meanwhile, are a little trickier. Technically, their new forms are called "Ancient Devolution," though that name might be different in the English release of the game -- remember, this is all translated from Japanese. The new forms for these legendary Pokemon will have some sort of prehistoric tie, which explains why the box art made both Pokemon look slightly different from their normal forms. Looks like the conspiracy theories were right!
Additionally, some of the story for the remakes will revolve around a character trying to dig into Mega Evolutions, but details are scarce right now. Team Aqua and Team Magma both make a return as well, though that's not exactly surprising.