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They raise the baseline for the lowercase keyboard, which I find very very bothersome. It seems as though they try to center the baseline-median area, rather than just stick with the baseline from the uppercase keyboard.

I accidentally misattributed some dislike for this to dislike for the San Francisco font; after I realized a bit more what was going on I'm slightly more comfortable with the font.

It does look bothersome, but if they moved the baseline down, then the 'q', 'g', and 'p' would be the problematic ones (they already look "too low" out of context with the rest, even shifted up).

This may also be apparent because in iOS 9, the letters are in lower case. They were always uppercase before the update.

Now you said that, I agree. I am unable to "un-see" it.

What keyboard, if I may ask? Do you mean the iOS on-screen keyboard? Or the real keyboard?

The iOS on screen keyboard. The lowercase version.