From the very beginning (see here), the idea to have to "pay" with your reputation points to set up a bounty makes me cringe.
But "featured question" is obviously a very good idea, and I welcome it.
However, rather than to see one's public reputation points slashed by a bounty (for instance, going from 3000 to 2500), why not have a separate private "bounty points" in one's profile, by default equals to your reputation? (and visible only by the SO user).
If you set up a 500 points bounty, that private account diminishes, not your current rep points.
If your public reputation grows again (by, for instance, 200), your private bounty points grows also (by 200 points).
That way, your public reputation, which should represent the value of your participation to the site, is never affected by your bounties.
However, bounties would continue to be limited by the total points of your reputation, just like today.
Any other rules currently in place for bounties would still apply, unchanged.
Before submitting this to UV, I wanted to test this brand new metaSO ;)
Plus I can edit my question on meta, which I can not do on UV!