What are the biggest challenges for GA airports?
One set of challenges that comes to mind are the types of things you find at an airport that is on that cusp between having an operating control tower and not.  I fly out of KJYO, Leesburg, VA and it very much fits into that catagory.  It frankly just gets too busy sometimes to support operations managed only by pilots coordinating on CTAF.  Examples of this include:


Wind conditions causing a conflict over whether Runway 35 or 17 should be in use.
Pilots doing straight in instrument approaches, while VFR pilots do pattern practice.
Conflicting planes on the single taxiway.


Indeed, I think the FAA understands this, since they are using it as the first US test site for a remote control tower.  The several times I've flown when this was in operation where a breath of fresh air!