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Note: Not references to other Pokemon games! (Like Jasmine being in D/P)
Note2: If you dont want to you don't have to include Pokedex entries!

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I've got a whopper of an answer coming, just have patience.
I caught a biggun!

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Well, here's ONE obscure reference that I found. I already answered a similar question with a similar answer. If you want more information, read there. I will not be including every reference ver, just the first that came to mind.

I assume by now you know that ORAS takes place in an alternate universe to the original RSE, correct? Well, there is a possible link connecting that universe (XY/ORAS) to the anime universe. Allow me to explain.

In the Delta Episode, Steven Stone mentions remembering that he fought alongside a Trainer and his black Charizard. Normally you would brush this off simply as old rock-collector gobbeldygook. But, in the Mega Evolution miniseries we find that Steven did, in fact, battle alongside Alain and his Charizard, who could Mega Evolve into Mega Charizard X. This means that the Steven from the games could have actually battled with Alain.

What ties this to the anime? In the very first episode of the Mega Evolution special, the little girl with the Chespin (forgot her name…) tells Alain that a Trainer came to Professor Sycamore's lab and calmed a raging Garcomp. What was that Trainer's name? Ash.

Also, the Shiny Beldum event from the beginning of ORAS has an OT of Steven and is holding the Metagrossite. In the Mega Evolution special, Steven's Metagross is Shiny and can Mega Evolve.

This theory is not ironclad. But it is a cool one.

edited by
There was a reference to DBZ (famous show, for those who don't know) in X and Y. Merely the statements "it's over 9000" and someone asking whether after mega evolution does the pokemon's hair become "yellow and spiky", but reference nonetheless.

EDIT: btw I just realized, this list is not even close to complete... you've just limited it to Pokemon anime.
I said I had ONE idea…
Dude you left out so many references and just left it to the mega evo special... Gastly can topple an Indian Elephant, other pokedex entries from firered refer to the realword. there's sooo many references .-. especially in hg/ss and x/y/or/as.
XD I remember that! I dont know much about DBZ but now I get the "yellow and spiky" referenc!
It is just… one… example. I did not intend to put in every single reference ever.
1 vote

In one Pokemon Movie, Brock asked if there were still vikings, and Ash said he thought there were some in Minnesota.