I actually think this would be a great idea. Pokemon from Gen 1 and 2 would have...no abilities. SHOCK AND AWE. But X & Y could have an ability to change abilities, or gain one, for every Pokemon.
Old movesets really isn't a huge issue. It only creates a different meta-game.
VC releases of Pokemon will happen eventually and Pokemon Bank being linked to the older games would just be great for multiple reasons.
1. Those games have a LOT of nostalgia attached to them. Matter of fact I could see a lot of people who don't like newer Pokemon games, they buy Pokemon Red, and then later on they learn they can transfer the Pokemon from Pokemon Red to Pokemon Bank and then to Pokemon X & Y and that's like, "HOLY SHIT MY ALAKAZAM CAN BE USED IN 3D GRAFFIXS." This allows nostalgic players to get attached to Pokemon X & Y, which believe it or not a lot of them think you can't use old Pokemon in newer Pokemon games.
2. Money. More options, more of it. Nintendo isn't going to lose anything by releasing these to the virtual console. At worst some butthurt Smogon fags but they'll realize it really isn't that bad and there's actually downsides to using Pokemon from older gens.