How can I change the order of secondary characters (or letters)?

Currently, it is not possible to rearrange the secondary letters. While I can't say if this will become a feature in the future, I'll certainly pass along the feedback for you.

I second this. Unfortunately the order of accented letters does not correspond to the active language so most common characters are hidden far behind rare ones.

Allowing custom order might be ideal, but i imagine could be difficult to setup in a user friendly manner.
I would propose following alternatives:
1) allow order definition via modification of some config/mapping file (mainly for power users)
2) prepare one config file customized for each locale so each user can have sensible default but still could tweak this for special cases
3) reorder accented letters based on their frequency (even ordering on global frequency across all languages will be an improvement)
4) reorder accented letters dynamically based on their usage by the user

Is this done yet?