Wally
I suspect that the software you are referring to is Nikons View NX 2, which incorporates a file transfer function. Possibly you are using View NX-i, but I believe that is actually a beta app although Nikon does not say so. It seems strange that NX 2 and NX-i, which are broadly similar and serve much the same purpose, should both be available. Whilst I am not an expert on anything Nikon, the impression I gain from reading people like Thom Hogan is that Nikon's software leaves a lot to be desired. If the applications are doing what you want, then all well and good, but I would be surprised if there are functions which are omitted from Lightroom.
One thing I saw from a recent article on one of Hogan's sites is that there is a new module to correct lens distortions, which looks as though it could be of interest to those who own Nikon lenses. It's very unlikely that there will be support for third party lenses, though, which is where the likes of Adobe have an advantage as they are brand agnostic.
http://www.dslrbodies.com/newsviews/nik ... tware.html