They aren't banned in OR/AS, but rather by Smogon's tiers and regulations. If you're unfamiliar with Smogon and their tier, Google it; they're special rules and regulations for competitive battles that help balance the game and attempt to give every Pokemon an environment in which they can be useful. They don't affect wifi battles or the main storyline of the game at all, only players who choose to play competitive battles with their rules.
Smogon's Overused tier (or "OU") is their most popular tier, and is the one that is the most like wifi battles in OR/AS since it allows most of the same Pokemon and bans the same powerful legendaries that the game bans. However, some of their decisions and bans differ from the game, and Genesect and Mega Lucario are two examples of this. They were both banned from the Overused tier and moved to Ubers, the tier above OU where all the powerful cover legendaries reside. They were banned as they were decided to be unhealthy for the OU game and the Pokemon in it by Smogon. Mega Gengar, Mega Kangaskan, etc. were both also banned a similar way. Smogon's rules do not influence the main game, but only battles played using their rules. Whether or not you follow Smogon's tiers and rules in competitive battles is entirely up to you, but keep in mind that a majority of competitve battles do follow Smogon's tiers.
If you want to play competitve battles with Smogon's rules, check out http://pokemonshowdown.com. It's the best online battle simulator out there, and most competitve battlers know about and use it. Just remember that until you're experienced with competitive battles and know how they work, you'll most likely get destroyed by the more experienced players who use the site.
I have an answer to a question in the following link that breaks down (most of) what you should know before playing competitve battles, if you're interested. It's an entirely new aspect of Pokemon battles that you should really check out if you didn't know about it already. :)
http://pokemondb.net/pokebase/231661/can-someone-explain-break-down-competitive-battling-to-me
