There's a reason for that, though, says hardware producer Hideki Konno and that's backwards compatibility with the previous hardware, the DS. Making it compatible with both resistive and multi-touch simply wasn't in the cards due to current technology according to Konno. One might also wonder how much price was a factor, the 3DS is Nintendo's most expensive portable to date at $250.
What furthers the touch screen mystery is why Nintendo is yet again falling back on resistive tech for their upcoming Wii U. The tablet-like controller shown off at E3 utilized the DS-era technology, stylus and all. That certainly has nothing to do with DS games, so it fuels the idea that price is a concern for Nintendo, and so is selling hardware at a profit unlike other companies who generally take a hit until the chip prices come down over time. Software sales fill in the profitable gap.
Nintendo is a company that seems to have fallen into habit, innovating where others are refusing too, yet skimping on the grandeur of modern technology. It's an odd in an industry known for pushing forward and in many ways becoming the determining standard in computing power with each generation. Nintendo, they feel safe holding back, letting the pieces fall where they may. Since the Wii was a success, maybe they're onto something, '90s touch screen technology or not.