Apples and oranges. Cambodia was a tiny country and still is a tiny country. Its people share much more of common heritage than "Chinese" people three millennia ago. Whereas Cambodia in '76 can be described as a stage of multiple warlords, China during the early times are distince countries with different culture, heritage, language, etc. The two cannot be made into common comparison.
A far more suitable comparison would be China and Europe. For example, if the Greeks and Romans had the strength of culture to keep their empires together, that would be a western version of China today. Thus, you are selling the first emperor far short of what he deserves.
Not to mention the man is an administrative genius. Much is made of his conquests and little made of his other achievements. To ignore this is to be short sighted. Overall, I'm not certain that he is the greatest (the topic being subjective and all) but he certainly is right up there. Hell, he would even be right up there in the entire world, not just China.
Furthermore, regarding his bloodline, I suppose you are referring to Lu Buwei. Let me remind you that it is nothing more than a myth. There was never any evidence to suggest its truth thus I don't think it holds much water.
But even it were true, it says nothing about Zichu's intelligence. You get a woman, she gets pregnant 12 months later and you are supposed to doubt the kid is yours?