At the moment that isn't known since it's not known whether Omega Ruby and Alpha Sapphire will even have Wonder Trade in it or not since there's no guarantee of it but if Wonder Trade is in it then logically it should be able to connect but there would also be the technical issues of things like Sceptile's Mega Evolution not being in the programming for X or Y which would be an issue but they could get around that by blocking things in Omega Ruby and Alpha Sapphire that aren't in the programming for X or Y. Like for example they could allow Mudkp to be Wonder Traded but if it is holding a Mega Stone like for example Swampert's Mega Stone that doesn't exist in the programming for X or Y then it would be blocked from being traded.

No one knows yet.