Because the specs were so close people were saying the mini was just an iBook without the monitor and keyboard, but with a $600 difference. I believe the major argument was the iBooks should have been a lot cheaper because it shouldn't cost $600 for a 14" monitor and keyboard, "the only difference" between the two. Keeping the Mac mini a feature or two behind the MacBook drives home the point it is an entry-level Mac and doesn't have the latest and greatest components.
I see what you're saying, but still disagree with your basic argument... hopefully in a nice way!

Two major points:
One, costs are more than the sum of component costs. For example, in general notebooks are harder to design than desktops, even ones like the mini, because their operating conditions are more demanding and there are more components requiring tighter integration. So despite the "same" hardware components, Apple needs to invest more fixed cost in designing, testing, and manufacturing a notebook than it does a desktop.
Two, despite the fact that the hardware components might be the same, the mini and macbook are still in different market segments. You can charge $$$ more for a notebook because the market has proven that people will pay for the portability, built in-screen, etc of a laptop... this is true for both PCs and Macs. Successful companies don't price based just on cost, they price based on perceived value, and consumers will set their own limits for that.... which is why Macs in general are more expensive than PCs, black macbooks are more expensive than white, etc.
People looking to buy a macbook have a different set of criteria than people looking to buy a mini. Could there be some overlap? Sure, but I doubt it's anywhere near 100%. And if the difference in those segments is non-trivial, then there's not such a need for an engineered differentiation between a mini and a MacBook like you're suggesting: no matter what their components are, they're already differentiated. If anything, it would be the MacBook that could cannibalize mini sales, as it could do everything the mini can do and more! With the exception of size of course, which is no small value so to speak....
My guess is that Apple's decisions for the mini were along the lines of, "Look, we need to update the mini to run Leopard, we don't want to charge more than $799, we want to keep our profit margin at X%, we don't want to increase fixed cost via design of new motherboards, etc. so what features can we sell?"
And out came what we have now! Which has probably already cost me significant $$$ in lost productivity by writing about it so much
