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The "Bond Phenomenon" is the real megaevolution, Greninja is just the only pokemon discovered to have an ability that bonds him with his trainer's feelings so hard it experiments the evolution, other pokemon lack of this ability so the only way they can awake the genetic potential of their species is using mega stones, that also explains why Greninja's change is superior (it gets +110 BTS and an upgraded move, while Megas only get +100 BTS).
The reason for Greninja's megaevolution to not consume your "mega slot" is clear if you read the manga, the megaevolutions you can use are limited to your Key Stone, so your character only can megaevolve one pokemon per fight with its only Key Stone, even if it's a special pokemon that doesn't need its own megastone (Rayquaza), but Greninja doesn't need a megastone nor a Key Stone so you can spam the Bond Phenomenon with several Greninja if you want even if it's a megaevolution. Not to mention that Greninja's transformation sequence in the games has the same purple sphere of energy surrounding him as the pokemon that megaevolve with stones, it's just partially hidden by the water Greninja generates
