Right, you are asking for a comparison of software that does two different things so it would be impossible to make that comparison.
nukeSEO is geared towards user definable meta tags and providing a dynamic site map for your site.
GT NextGen is a script which re-writes long url's and converts them to a more memorable and easy to follow url.
They both have their uses but for different things.
As GT NextGen has not been updated in what must be a couple of years now, if you wanted to go that route, check out
www.montegoscripts.com ShortUrls module.