I'm not suggesting it be a permanent ban. But if you flunk a test a bunch of times, obviously something isn't right. I think some requirement for hands-on training is very sensible. It might also discover some physical reason for the problem. Maybe the dude is blind in one eye or something.
It's not like basic driving skills are especially difficult. I suspect parallel parking would be the most difficult to master for many. So send the flunky off to driving school where someone sits with him while he figures out how to park properly. I can't see that being a legal problem.
As for the rest of your question, I have no clue about pilots, but I do know a little about (commercial) marine licensing. It's much like a graduated licence beginning with smaller displacement vessels and moving up. Each step requires sea time under the supervision of a more qualified person. Once those hours are completed and logged, the candidate can move up with more courses and then more sea time. There are no shortcuts but that's not really comparable to driving a car. To get a boaters license, it's either an in person course or online, followed by a written, but unsupervised test. A small boat operators permit isn't really about the skill to pilot a boat... it's strictly rules of the road and safety requirements. There isn't a "road test" at all. But then bombing around on a lake isn't much like driving down the 401.