Now that I think about it, there was an interesting reference one of the trainers make in Reversal Mountain. After you beat a battle girl in a triple battle and talk to her she calls her 3-Pokemon fighting style "Jet Stream Attack" which is a combat formation in Mobile Suit Gundam.
The magma and water differences in Reversal Mountain are huge references to Ruby and Sapphire, lol...
It's not an Easter egg, but I love how Professor Juniper evolves her Minccino into Cinccino *u*
Also, one of the preschoolers on Route 3 says the same thing he said in BW, something like "Let's go! Hyper Beam!!"