One thing that would indicate that our methods are fundamentally flawed is if YcA and ME came out as living at the same time or if YcA lived before ME.
I know I'm replying to something posted over three years ago, but I only just read it since this thread's been bumped, and felt obliged to plow in.
Calculations showing that Y-chromosonal Adam lived before Mitochondrial Eve would not indicate any fatal flaw in the methods. It may be more a priori likely for Mitochondrial Eve to be older, for the simple reason that successful males can have a lot more offspring than successful females. It's not, however, a definite fact.
And based on the information we currently have, it seems that it's not true. Y-chromosonal Adam is substantially older than mitochondrial Eve. I'm surprised how little coverage this story has gotten, but a wildly divergent Y-chromosone lineage has been discovered by commerical DNA sampling, and further investigation has found it present at a low frequency amongst African American and West African men. This lineage is estimated to have split from other known lineages more than 300,000 years ago. Y-chromosone Adam, it seems, was not an anatomically modern human.
It's been suggested this could be the result of introgressive hybridisation with another species of human in West African prehistory, just as seems to have happened with Neanderthals and Denisovans outside Africa. The difference is that this particular hybridisation event has resulted in strict patrilineal descendants still living today.
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