Zacian apparently may be giving Mega Rayquaza a run for its money. But when the Gen 4 remakes come around, I completely expect Dialga, Palkia, and Arceus to be buffed in some way and overthrow Mega Ray. Maybe Giratina as well, but Pokemon Platinum exists. Just don't expect Mega Rayquaza to be the most broken Pokemon after the Gen 4 remakes arrive.
