I have never been as much of a typography and kerning wonk as maybe I should be, but the new iOS 9 lowercase keyboard feels wrong to me. (A lot of people don't like the way the keycaps swap, but it may be a matter of people getting used to it.)
Here is a sample:
I made a quick Processing.js program to try to explore the idea, and came up with this:
Red lines are geared at the uppercase boundaries, blue line for lowecase. In my Processing you can press the button to swap upper and lower.
The lines I tried to draw might not be perfect, but it still seemed to reinforce my intuition... in short, it feels like Apple used the centering relative to the uppercase, and sometimes that feels off. Maybe to reduce the jarring-ness of the transition when you toggle from one to the other? Characters such as "f" "t" and "y" feel especially off to me.