I'm almost 100% sure Articuno will be in Ice Cave (right after Mahogany) :P
Wouldn't be suprised if Zapdos was still in the PP... or possibly in some extra room in the Lighhouse.
After Moltres could go in Burned Tower (somewhere) or even Victory Road???
I don't think so, since the 3 Dragon masters say that a Legendary DRAGON pokemon is on top of Ice Cave.
So Probably Rayquaza.