Well, unless navicore is free and open source I see quite a few reasons to continue. Competition is good and any time you have a single choice it's not the best situation, whether it be in regards to features or bugs. Besides, MM is quite capable for a from-scratch program for the platform. I've used it many times, and if nothing else a map with a dot "You Are Here" and breadcrumb trail is invaluable.

As far as the RFC I would definitely move away from the file/directory-based structure. If nothing else it would make it easier to a copy a single DB file (i.e. if you went with SQLite) than a million tiny ones. I would also be curious to see which DB engine you might choose since obviously it can't be too big, but performance might be marginal for some of the simplest ones.

Keep up the great work!
Larry