I really think the B-Spec points you acquire will determine how good your B-spec driver is, and I'm pretty sure it says that in the instruction manual. Having said that most of these complaints about the driver come from people who probably never use B-Spec except in the endurance races, then tell their B-Spec driver to go out and drive a LMP at la sarthe and are surprised how terrible it is at passing, or can't stay on the road...
So, if you're only going to use B-spec for endurance racing you'll need a car that is vastly overpowered so you can set the driving on 2 or 3 which will allow the driver to driver at a moderate pace, but since the car is so fast will be faster than your opponents fast pace, or else you'll need to give your B-spec driver some seat time. The more seat time he gets the better he'll be, note that you'll get B-spec points regardless of where you finish (even in 6th). Consider him like a person who needs practice, you wouldn't expect one of your friends who has never played a GT game to take over from you and maintain your pace and pass at every opportunity, so you can't expect the b-spec driver to do it either.
It seems to me that machine skill is how well your driver is able to handle more powerful cars if you start it off in slower cars then build him up you'll probably have more success.
Course skill is probably how well he knows the track, the more seat time, the higher this will be as it learns the braking points and racing lines, as you'll all aware there are only a dozen or so different types of corners a track can have, so learning the racing lines for each type of corner will allow you to drive fast on any track once you sort out which type of corner you're heading to -- consult your original Gran Turismo maual on cornering, etc.
Battle Skill is the big one for passing, it seems that the higer this is the better your driver is at passing and avoiding being passed. Maybe someone could test to see if this increases more with a overpowered car that passes opponents easily or a underpowered car that has to work and drive well to pass opponents, or if it's just the number of passes that raises this value.
All of this is speculation on my part but I haven't heard a better explanation anywhere.