1) It is (comparably) cheap to manufacture an individual chip, but it costs billions upon billions to design a new kind of chip, create an infrastructure to manufacture it, market it, and sell it to the public. Therefore, it is more cost effective for a CPU manufacturer to have fewer lines, as long as the company can maintain good market segmentation.
2) As with any product, there are defects in manufacturing, and not every chip comes out perfect. However, the CPU industry, along with other computer parts industries, has gotten around this problem of waste by disabling the ineffective cores and rebranding them as lower end chips. As the manufacturing process for a single line gets more sophisticated, the binning process switches from arbitrary to planned.
3) Intel has decided to move the binning process from the hardware to the firmware level (I know those may not be the correct terms; just go with it.) Instead of having to ship OEMs a huge supply of potentially wasted chip varieties, Intel can ship them a ton of the same chip, and the OEM can simply upgrade customers at checkout, probably paying Intel a fee a la carte. Similarly, if a customer either doesn't want HT on a certain chip, or does but can't afford it at the moment, this allows him to buy the chip now and upgrade later, as opposed to having to save up and wait or buy an entirely new chip a few months down the road. As long as pricing levels are concurrent with functionality levels, how is this in any way a bad thing? It seems incredibly convenient.
I know this is long, but there are two additional points that need addressing:
4) A lot of people keep saying that the reason the practice is EVIL is that it is not a physical limitation of the chip, but rather an artificial software limitation. Yes, I agree there is a difference there. What significance does it have? As long as Intel advertises the limited chip with the proper feature set--and charges accordingly--how has anyone been ripped off, except people who either don't research their purchases or expect a top-dollar product for a bargain basement price? It's like buying a 360 Arcade and expecting a 250GB hard drive to come with it.
5) Everyone keeps saying that it's "idiotic" or "naive" to assume that Intel will price the limited chips according to functionality. I don't appreciate being called an idiot, so I ask: do you understand economics? If I am Mr. OEM and Intel tells me, "Hey, we're going to sell you these chips that can be upgraded to all these various speeds, but we're going to charge you the maximum price for all of them," I'd be making a call to AMD in the next ten minutes. I'm sure that, unless OEMs are just monumentally stupid, the various companies will work out new purchasing/sales models with Intel. Of course Intel will try to make the most profit out of it, but so will the OEMs. Assuming, of course, this goes mainstream, which it probably won't, because people are so happy to be offended these days.
Overall, I think all of this uproar stems from an unwillingness to try new methods of sales and purchasing, a general aversion to large companies in general, and the strange disease of the Internet that seems to breed outrage and moral indignation every time some rich guy doesn't remember to put the toilet seat down.