It seems to me that some sprites are pixel perfect on my iPhone 5 and some are not.
Well, that is interesting.
Everything should be pixel perfect, with some small exceptions - like the background of the sky which is half size.
Some of the textures are stored compressed (backgrounds) and some uncompressed (chicks, bird).
The primary limitation that forced us to do things at a certain way, is the fact that you are stuck with either a low quality compressed texture or a too large uncompressed texture. There is no good middle ground.
One of the features of 2D Toolkit that saved the day for me, was the ability to dice sprites.
If you see artifacts or a blurry chick, that is not intended at all. So if you have a screenshot of what you mean, it would help me understand if its by design or a bug.
EDIT: I see the difference in quality for the running chick and happy chick, I am investigating the cause. All sprite settings seem the same, will look deeper...
Here is a small screenshot of the problem.