I have some ideas for some storyline differences.
-The mascot that isn't for your game will probably be obtainable at some point. Probably at the bottom of the cave of origins after certain conditions are met.
-If you're playing AquaSapphire, Team Aqua will attempt to capture Manaphy at some aftergame location. Probably in a dive cave on one of the Ocean Routes. If you're playing MagmaRuby, Team Magma will attempt to capture Heatran at some aftergame location. Probably a cave in the desert.
-After obtaining the Regis, Regigigas will be available in a hidden Passage of the cave you unlocked the Regis with.
-At some aftergame location, you will find N. Probably saying something about trying to "Find Himself" and engages you in a battle. Whether he would use the same Team as he did in BW I am unsure about. If so, he will use Reshiram in MagmaRuby and Zekrom in AquaSapphire
-Zekrom will be available at the top of Rayquaza's Tower in MagmaRuby after Catching Rayquaza and obtaining the National Dex. The same would go for Reshiram in AquaSapphire.