It's almost guaranteed that there will be backwards compatibility. If anything gen VI appears to only be a graphical overhaul more than a game data one, and then we all know how the Gen III thing went...not that it was entirely their fault for FIXING the series but still...best to avoid such a meltdown.
What I'm hoping for is a free app for the 3DS which will work like a Box RS thing for transfers; choose all pokemon you want to transfer in your Gen V game (boxes at a time if necessary), it saves to the app and to the cart, then you insert your Gen VI cart and choose in the app or game to transfer into the game. On a side note, it really is about time to get rid of the banning of transferring HM-knowers. That's just illogical, and then there's the item thing. Yes, I know you don't necessarily want us to bring in 100 pokemon with master balls, but either way cheaters will get our balls so don't bother stopping us from BRINGING ALL ITEMS in.