Anyone else notice the FMS doesn't contain smaller airports, making flight planning almost impossible. For example, F97, F53, etc, don't show up in the FMS.

I think that's normal. Navigraph/NavData Pro may not contain data for those small airports. You can still put a nearby airport as your destination and use an actual VFR chart to navigate. IMO it's not that strange. I remember even in 737's FCOM there is a section talking about the procedure to fly into an airport not in FMC database.

Try putting a "K" in front of those ICAOs. KF97, KF53, etc.