The core d20 Modern Martial Artist makes a good generalized fighter, whereas the B&F classes help their characters acquire more maneuvers and masteries. Consider it the difference between someone schooled at a modern, classroom-style dojo in a contemporary version of a style, and someone training one-on-one with an experienced sensei (or however this analogy applies to the martial arts style in question).
It's just like when running a Blood & Guts game... I don't ditch the core Soldier. That Soldier AdvC is one way to do things... the B&G "Training" classes are another.