Any chance the pool settings could be stored in a separate configuration file? It would sure make changing those in bulk/on multiple rigs a lot easier, when my pool preference order changes... distribute one pools.conf to each rig.
It also would be nice to have an ability to re-order pools from within cgminer.
I've got 3 BTC in bounty for each.
Can I have the 2nd one

With the API, you simply move any pool of choice to position 0 (highest priority).
The number of moves to get the required order is at maximum, the number of pools.
How many pools do you have anyway?