The 3DS isn't comparable to a Vita in terms of graphics or probably raw horsepower, but those are things that never kept the old DS from selling like gangbusters. So why would Nintendo officially obsolete their launch platform by adding a second stick to it?
My guess is that the developers wanted it, and wanted it really badly, but that's not normally how Nintendo works. They make the systems, they make their own really good first party games... ok, maybe some of them are really good... for their systems, and if third party developers can make good games they can sell them too. If developers are angling for cross platform Vita and 3DS development, a second stick is really a must for that to make sense, especially since the attachment and future version of the 3DS with both of these things built in also gets another shoulder button. There's also the idea that the battery compartment will get bigger, allowing longer battery life.
Did Nintendo actually come to the realization that they needed better control options for this platform to avoid it sinking under the weight of re-releases of everything that was on the DS with no real innovation other than maybe passable 3D visuals? How would this ever matter to Nintendo, the masters of remanufacturing their very strong (and even not so strong) franchises onto each successive platform with success?
So is the idea of twin-stick parity for the 3DS bad news for Sony on the heels of a price cut? I doubt it. They're still different enough animals hardware-wise, and the Vita isn't going to succeed based on the hardware alone. It's going to be the software that sells it, and we won't know more about that until it lands stateside in 2012.