Kindle has a web browser, which Nook lacks (unless 'you hacks'). Storage is more limited but between 5GB personal documents storage, and ability to access dropbox, calibre server, etc. with the browser makes it more flexible and convenient if you have 3rd party content.
Nook only has something like 250MB for 3rd party content unless you add SD card, and it all has to be managed over USB.
Of course comparisons of screens/lighting is pretty hypothetical at this point, as only Nook Glowlite exists in the wild. And I think we can anticipate a new Nook before the holidays with at least XGA screen. The limited comparisons we have with NGL and KPW seem to favor KPW however, as they should, or Amazon would be silly to ship KPW.