I don't use a QC 2.0 charger, so I'm just guessing, but it sounds like thermal throttling. When the phone's internal parts reach a certain temperature, the software dials back the CPU to give the heat a chance to dissipate. My phone gets fairly warm when charging (with the standard Moto charger), especially when charging a near dead battery, but I've never noticed it slow down. It would be reasonable to assume that because the Quick Charger puts so much energy into the battery in such a short period of time, that it would cause the phone to heat up more drastically.
Again, this is just a guess. All the reviews/info I've read online regarding quick chargers have said they are safe and shouldn't damage the battery over the life of the phone, but none of them mentioned any thermal throttling.
I would recommend buying the Moto brand quick charger to see if that has the same issue. I think you can probably get them at a carrier store (VZW, ATT, Etc) and then return it if it isn't any better than the Aukey.