AA,
Yes, understanding Mitochondrial Eve correctly takes some serious thinking, and perhaps some charting with a pen and paper. For those who have not yet read it, I recommend that you read this page carefully. It does take work. I had to turn this over for a few days before I accepted and understood it fully.
Euph,
Yes, I think you're right. I'm totally sympathetic to the scientists because in my experience programmers tend to do the same thing. We want to choose terms that are clever and punny and hopefully metaphorical, because they help to make a subject more approachable. In my last project I wrote a specification for a project we playfully dubbed "Munchkin."
After reading aniron's comment above (which I knew was inevitable going into this thread), I began thinking about this tendancy of creationists to pick out bits and pieces of science that they like while ignoring where the science actually leads, and it struck me as enormously intellectually dishonest. Mind you, when I was a Witness, I know that I was guilty of the same thing. But if you're going to read the science, then you ought to read and understand all of it, not just pluck out words and phrases that seem to support your point of view. On the one hand, such a person appeal's to science as an authority, but on the other hand, they don't truly care what the science is actually showing. It's just a tad ironic.
SNG