This is how I see it.
There will always be hacked Pokemon in the video games and I don't think X Y will be an exception, nor should it. Action Replay for the 3ds or not, people will find a way to hack and get what they want regardless. If someone wants to transfer a full national dex from bw/bw2 over to X Y, why do you care if they actually caught all those Pokemon or if they hacked them? It is their game, why can't they do what they want?
Oh wait. Yeah. Fighting a team of hacked Pokemon isn't fun, is it? Then don't battle people who hack. Battle people you know don't use hacked Pokemon. I don't battle random people for that very reason. Getting a hacked Pokemon via GTS shouldn't be able to happen, and if it is a hack that makes it through (i.e. has proper moves/abilities/PID/whatnot) then what is the problem then? Breed a new one, and release the traded hack. Or better yet find a trading community full of trusted members, and set up trades with them!
The Pokemon virtual economy? I understand trading in Pokemon games, but if it is just going to be people wanting to trade version exclusives for ridiculously high level Pokemon, then what is the point. (And don't say people won't do that, at the start of gen 5 people were demanding lvl 50 Golem for a level 22 Gothita as an example). In other Pokemon trading communities what I have seen is if you have anything remotely rare or somewhat valuable, you are allowed to make outrageous demands for it. It should be, I'll breed a Chespin for your bred Froakie
, not I'll breed a Chespin for a lvl 50 Garados
. But you give people that right, you can't really stop them from trying.
Pokemon X Y will be backwards compatible with bw/bw2 at the very least. It may not be ready at the launch, but I hope it will be. I hope they will implement some type of legality checker when transferring Pokemon. I know I am not the only one that wants a system in place to make sure you can't ask for impossible Pokemon on the GTS. I look forward to a better GTS and no one wanting < lvl 9 Resharim.
TL;DR Hacked Pokemon will always be around, sorry but it's true. Don't battle or trade with them if you don't want to. The virtual Pokemon economy has been broken forever, and I hope they can fix it in gen 6. Backwards compatibility will be implemented, they already said they were working on it. I hope XY will be as awesome as we are all wanting it to be.