In Kalos games they apparently know it's kind of negative for the Pokemon to be mega evolved but for some reason they keep it hush hush from you.
Let's read some dex entries.
Mega Lucario:
>It readies itself to face its enemies by focusing its mental energies. Its fighting style can be summed up in a single word: heartless.
>Its aura has expanded due to Mega Evolution. Governed only by its combative instincts, it strikes enemies without mercy.
Mega Metagross:
>Its intellect surpasses its previous level, resulting in battles so cruel, they'll make you want to cover your eyes.
>Mega Evolution stimulated its brain. It emerged as a ruthless Pokémon that will clutch at any means of ensuring its victories.
Mega Salamence:
>Mega Evolution fuels its brutality, and it may even turn on the Trainer who raised it. It's been dubbed "the blood-soaked crescent."
>The stress of its two proud wings becoming misshapen and stuck together because of strong energy makes it go on a rampage.
Mega Gengar:
>It tries to take the lives of anyone and everyone. It will even try to curse the Trainer who is its master!
The reason they quote that "represents the bonds between the Pokemon and its trainer" is most likely because it's basically a self harming, unnatural state of self; indicative that it's willing to go to that far, just for you. That would also explain why are they tied to the Ultimate Weapon or whatever it's called: they were inventions whose purpose was to wage that ancient Kalos war, regardless of the wellbeing of the Pokemon.
Why they present it to you, an irresponsible, budding trainer from Kalos who is likely going to abuse it, is beyond me.
