I just took a series of pictures with several camera apps of both my rabbit and some outdoors shots of a bush and grass. It may be my imagination, but it appears that the noise reduction has been reduced slightly. It's still there. I noticed no quality boost from Camera + and Camera Plus by rookie. In fact, these apps were more annoying because they wanted to process and slap filters on each shot. No.
The only app that provided more clarity was Cortex, but as mentioned previously, your subjects need to be still. Cortex isn't a traditional point-and-shoot app, it's more of an image processing app. Still, I managed to get of my shot at the same angle (on the floor) of my rabbit's side while he was laying down with the stock vs the camera app. The stock app size was 2.7MB and the Cortex image was 28. I have attacked a screenshot of the zoomed in images (too big to upload and I'm not cropping right now). The stock app is on the left and Cortex on the right. Honestly, Cortex was a little better with the fur, but not immensely better. Where you really see a differences is the clarity of the background with the Cortext app.
Still, maybe it's me, but I feel like it is a little better. Also, I was looking back through some images taken with my 4S. At a glance, the iPhone 6 images almost all look better because of faster focus and better exposure. When I zoom in to 4S images with bad lighting I notice the same blur effect as the iPhone 6. The difference comes in okay-well lit environments. Generally, the 4S had worse focus and more noise grain, but fine details like fur where retained. On the iPhone 6 the images where usually sharp with notably less grain, but the smudge effect is more pronounced in fine detail.
My honest opinion: most of the shots taken in decent and even low light conditions look fine when viewed on an iPhone, iPad, and even larger monitors. To the common user (which Apple caters to), it's great. When you zoom in is when the issue become more pronounced. I wish they gave you control, because I'd rather get all grain and edit it later myself than have the A8 attempted to do it for me. :/ I hope this helped some one.
NOTE: I have two uploaded comparisons. In both, stock app on the left, Cortex on the right. The first set is a zoomed in version with iPhoto, the second is a normal view (no zoom). Mac rumors has file size restricts so this is somewhat difficult especially because the rMBP screenshots are large and I don't have an account with a photo sharing service. I realize that screenshots are not the best way to convey it, but there is no other way without making an account somewhere.