Heero was drilled to fight since his youth, so people often call him perfect soldier n stuff and always put the training as reason for his superior skill. But since SEED there are the Extended (aka human CPU), who have undergone even rigorous training since birth and are even optimized for combat with mind enhancing drugs and mental conditioning, which has maximized their perfomance at the expense of even their life span. Overall more extreme circumstances, with the and are supposed to beat coordinators as "natural" (yeah right) humans for Blue Cosmos. Since non-competitive Extended are supposedly discarded, does that mean the existing ones would be better pilots than Heero? Or does Heero have more up his sleeve (he's a protagonist after all)?
Note: The ZERO system and similiar non-pilot related things do not count as argument.