Well, what happened for us is that we actually came up with the story, then build the Prestige Classes around that story. Personally, I used to do is come up with the mechanics I want to do first, then fill out a background to fit the mechanics. Having a story as inspiration was HUGE for our success, I think, and it's definitely a lesson I took from that contest in designing; things are ALWAYS stronger when there's a synergy correlation between fluff and mechanics.