I think that it is more motivating for somebody to give a higher bounty, knowing that it will be closer to the top on the featured questions section.
Then, questions with the same bounties should be listed in chronological order.
I guess I'll shed some light on what currently happens. The featured questions are sorted by the time remaining in ascending order. So the bounties that are ending the soonest show atop. The point of the featured list is to show questions that have bounties, or are "featured" and to get eyes on those questions. If a bounty for 500 points has 4 days left and one for 50 points has just a few hours, which is more important? In the eyes of the system the bounty that's been hanging around for the last 5 days with no one awarded is far more important than the one that is higher.
Those who wish to sniff out the higher bounties can do it easily enough by skimming the list since it rarely grows larger than one page.