I own an old HTC Wildfire A333. I recently switched it back to the HTC Sense ROM and I saw that the quality of pictures taken with the default HTC camera app seem better. Not slightly. Quite a considerable amount actually. I know that picture clarity is related to the camera hardware. I switched back to CM9 again and when I turned the camera app on, I could see the clarity was bad(without taking pictures, just through the app interface. I did take pictures though and the quality was bad. The settings were all accounted for.). Even when I used another camera app the quality was pretty bad. Sadly, I couldn't flash the HTC camera on the CM mod to see if that's what makes the difference. My question is, does software affect the picture quality? If so, how. If not, any answer to this question?
Yes, software tweaks have a massive effect on image quality, and the htc sense version was optimised for you sensor, whereas the cm app wasn't, this is the difference between a well optimised app written to play to the strengths of a specific platform, and a general app written to give a moderately good experience on average. This same thing can be applied to cm more generally, with apps that use specific hardware (e.g. dialer) often having a worse experience compared to stock.