Pokemon Bank and PokeTransporter have obviously detected that the Arceus has been hacked into the game, and have not allowed it to travel to your copy of Y. In case you didn't know, the apps have a hack tracking system to check whether the Pokemon is legal. It's not completely accurate, and sometimes allows hacks if there isn't anything suspicious about them (and even rejects real Pokemon sometimes), but it will never allow a Pokemon that has clearly illegal details, such as ridiculous stats, moves they aren't supposed to know, etc.
This hack system is most likely put in place to keep X and Y and future Pokemon games free of fake Pokemon, which will make legitimate players happy and keep hacked Pokemon out of official tournaments. The hack system is not in the transporting systems for earlier games like White 2 and SoulSilver, which is why your hacked Arceus got through those games.
So basically, your Arceus can't get through because it's hacked, and hacks aren't allowed. Go back to it with a real Arceus and see if it goes through.