Really comprehensive evaluation and I really appreciate it. I experienced the same thing with my unmodified HTC camera app - these makers seem to over-process and lose clarity.
Do you use the JB+ option to save in high quality?
It's been a few months since I've tried the stock Google camera but my memory is that feature was missing from it.
Based on your feedback, I'm even more interested in hearing or seeing JB+ results for the RGBC camera on the X.