The advantages, according to the Examiner (who talked to frequent SFist commenter Greg Dewar of the N-Judah Chronicles)? Service to Caltrain will no longer be the domain of the most popular line MUNI offers. Also, as two trains will now be servicing it, that'll mean more trains will be sent to the Caltrain. The bad news? All those people who live near the N Judah line partly because it took you directly to Caltrain now have to transfer. The other disadvantage is that the J Church is not known for it's timeliness as it has the worst on-time percentage of all the other MUNI trains as well as being one of the top five finalists in our Worst MUNI Line poll.
We never understood why the N Judah was chosen as the special bus that would take people to Caltrain. It might have been the most popular bus, but if you combined all the riders of the other trains, that would be more than the N. There wasn't really any excuse all the other trains didn't go that way, or at least more lines than just the N. That meant that most people had to transfer twice before they even transferred to CalTrain and that always seemed a bit much. Shouldn't public transportation be, you know, convenient?
Image from the Examiner