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at the start of the battle I throw out my Pokémon, it does it's cry, and just before I can select a move, it 'shuffles' on the spot. Heliolisk and Greninja do it, and it's in the rain. I've also spent some time in amie and super training. Do any of these things have an influence?

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This is because of your Pokemon's Affection in Pokemon-Amie. If your Pokemon are doing a small shake when they enter battle, it is because they have 2 Affection (the hearts in Pokemon-Amie).

This is just a little animation and doesn't do anything significant in battle; however, the two hearts will also give your Pokemon a 1.2x boost to their experience according to Bulbapedia. Higher Affection will give you more little bonuses.

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You basically said what I said
There was a three minute difference lol. I was typing this at the same time as you were, you just happened to post it before I did.
Oh and btw, you edited in the experience thing two minutes after I posted my answer, which makes me think you copied info from my answer. If that's the case, then you're the one who is at fault.
I didn't copy your answer.i was looking through the pokemon amie section in bulbapedia and thought that i should add that part.I saw your one after i added cuz my computer didn't reload when you answered.
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This happens due to high affection in Pokemon Amie(2 or 3 hearts). It's not related with Super training.There are a few other benefits to Pokemon Amie such as getting critical hits more often,enduring OHKOs,giving a boost in experience etc

Source and Source

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