(Faithful readers will notice that today's update is a little late. Er... I meant "business days"?)
I'm realizing why MongoDB isn't the absolute perfect choice for every application in the universe. And that reason is joins.
Some data just naturally lends itself to joins. With the way it's laid out, GTFS is very well suited to doing joins. Even the most popular MongoDB GTFS implementation uses Mongoose, so it's basically SQL.
I'm going to push on with MongoDB, although I can freely admit that it is a mistaken endeavor that should never be repeated.
Once I get my join problems solved, I look forward to submitting my app for review!