For the last slot, I would personally use a special move such as Surf or Ice Beam / Blizzard, since it allows Rayquaza to decimate Rhyperior (where I think it can take at least 1 Earthquake and decimate you with Rock Slide) and possible hit physical walls harder. It's not like Surf / Ice Beam would be weak anyways, he has that huge 150 Special.
Good point.
With 150 as both offensive stat, Rayquaza can go physical, special, or mixed (although IMO Physical is best because of Swords Dance). Damn dude is too awesome.