Few things come to mind:
1. Your budget. How much are you willing to spend?
2. Style. Do you like the 00 or 03+ R6's?
3. Mileage. Obviously, you're not going to find a 00 R6 new(nearly impossible). Do you mind getting a bike used?
4. Carbeurated (<--sp) vs. non-carbeurated. Correct me if I'm wrong, but weren't the 00 carbeurated?