While this would have made some sense, (they were getting into Rayquaza's territory), it also makes sense why he didn't show up to challenge the new dragons: He may still be in Team Rocket's base (remember his cameo in Pokemon Ranger and the Temple of the Sea?)
... well, at least Haxaourus there... otherwise the plot would no longer makes senses at all...
Updated
The Sword of the ValeIt's so cold... I can't breathe...Satoshi, hang in there!shiverWhat is that!?Something is approaching us rapidly.They're doing this now!?KiryuryurishiiiiisparkleIt can't be.Victini and
Zekrom Reshiram
RayquazaThis is getting too messed up.