As part of my latest eBook projects I'm working on updating the software sections to match Nikon's latest offerings. What I'm finding is what you'll see on the various Nikon Web forums: there are a lot of small bugs, workflow issues (especially for batch processes), and other idiosyncracies in Capture NX and ViewNX, even in the latest versions. On the Macintosh side, it doesn't help that the latest Apple OS release (Leopard, OS X 10.5) is causing developers of all sort some grief.
Now that Nikon is charging more for its software (and even though you got Capture NX free with your D3 or D300, I'm guessing you'll have to pay for the 2.0 upgrade), I think it's time that we demand better testing and less buggy releases and more attention to user requests. If you walk like a software company and talk like a software company, then you're a software company. Just as Nikon is a leading camera company, it's time for them to grow up into a leading software company, too.