Hell yeah! Turn the different version movies into a united sequel!
That sounds like the games actually...

This one got lost in the translations. Bumping.

It is said in the Pokedex that Rayquaza flies ENDLESSLY on the ozone layer. It took place on the ozone layer, it seems.

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...