I looked into whether geodatabase would be a good format for user data. Ie polygons, paths, waypoints that they draw, record, or import from GPX files or KML files or other files.
Based on licensing requirements, it is only good (for me) as a read only format. My customers are consumers and wouldn't pay $500 per license. I understand that the more advanced licenses are needed for editing a geodatabase, even just locally.
So what do people tend to use?
I've heard of something called Spatialite, but believe there would be complications getting it to build and distribute with .net.
I have used SQLite (without the spatialite extensions), since it is built in on mobile platforms like Android. But for querying purposes it was weak in two areas: finding polygons that intersect the screen and finding polylines that intersect the screen. The workarounds I've done on past projects were not pretty.