I don't have an iPhone 6 yet (my 6+ is arrive today) but as semi professional (part time) photographer, I have an idea as to what might be causing this aggressive noise reduction.
The first thing to note is that the lens on the iPhone or any phone for that matter is tiny in comparison to your average point and shoot or SLR. So straight off the bat, the sensor is getting less light. In good light (outside), the camera will get enough information to produce a decent picture. In low light though (indoors or in the evening) it will need to push what's known as ISO. This effectively increases the sensitivity of the camera's sensor but at a cost. The higher the ISO value, the more noise is introduced into the picture and as a result, a noise reduction pass will have to be applied to counter. The noise reduction does have it's advantages when used sensibly, but crank it too high and you end up with waxy looking images.
This may be one reason... Not saying it is and once I get my 6+, I'll be able to give a more educated reply, but this would be my first guess.