Are you talking about project presets or output presets? And what kind of camcorder is your source files coming from and what do you plan to do with the video once you output it?
The difference is in the exact CODEC used to Export these two file types. Many feel that the MPEG compression yields slightly higher quality, at the expense of less Duration on a BD. Others find little difference in the quality (depending on just whose H.264 CODEC is used), and like to be able to get more Duration via the H.264. Both are approved for BD use.
As for whose H.264 CODEC to use, most people feel that either Lead, or MainConcept's are better than Apple's, but in the end, it comes down to personal choice and budget.