For the last couple of battles, I've noticed that my Greninja receives boosted EXP despite never having been traded. He has also been moving from side to side at the start of battle since around the same time I noticed the EXP increase.
I've been to Pokémon Centres multiple times since noticing and it doesn't seem to be Pokérus (although I click through the nurse's dialogue quickly, so I may have missed it if it's not displayed elsewhere)
What could be affecting my Greninja?
Best Answer
While evolving a Sylveon for a trade, I stumbled upon a solution. Once I was ready to level up my Eevee, I noticed that he too was receiving boosted EXP. As it turns out, I had messed around Pokémon-Amie with Greninja and he ended up with 2 hearts of enjoyment. To verify this hypothesis, I played with a spare Gabite, defeating a wild pokémon after each additional heart.
With a single heart, there was no noticeable change to the Gabite: she still earned normal EXP and didn't seem to have the thelepathic abilities Sylveon displayed. Once she earned her second heart, she immediately started earning boosted EXP. She also starting dancing at the beginning of battle as Greninja had.
Earning two hearts of Affection in Pokémon-Amie will boost EXP earned for the beloved pokémon