People are too fussy. It's primarily a phone with a mediocre camera lens, no matter what software you use you will never get SLR quality. It's pretty decent at taking snapshots, amazing in fact that a phone can take pictures this good.
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People aren't talking about getting SLR quality photos... here's a problem with the stock camera app that causes it to over process low-light photos making them look blurry.
Note 3 captured the filth in my company keyboard
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I'm not sure I can take those people seriously. So far the complaints I've seen have been on pictures taken with the Auto setting, as if the camera had no other settings or adjustments that could be made.
Your question will probably generate a lot of opinions about various third party apps. I would suggest also seeking reviews of how the various modes on the default camera handle different types of pictures/scenes.
Ny Note 3. I don't remember a plastic protector over the lens. I am checking now and it doesn't seem like one is there.