Well, Pokemon that are obviously hacked (Shiny Victini with Frenzy Plant and Wonder Guard, for example) won't transfer.
Pokemon that are better made will probably pass; even an illegal move will probably get through.
There will probably be some false positives, though; in Gen 4, a bunch of people got upset because their legitimate Shiny Jirachis were being rejected by the GTS hack checks.
Illegal moves don't even get through the Wi-Fi battle protection of B2/W2, I'll doubt 6 months later they'll get through Pokemon Transfer.







