The 3DS actually reused the DSi power connector from 3 years earlier, which partly explains why it seems backwards. The other part of the explanation, which is also why the DSi had its own connector, is that it drew more power (4.1W) than the DS needed and more than USB could provide (2.5W). Arguably, Nintendo could have used micro-USB with USB Battery Charging (up to 7.5W) for the 3DS, but it would have meant a 3rd new connector and also more complex circuitry.