It's not a perfect film, by all means, but when you compare it to it's competition...
When I was beginning my edit of NSNA, I came to the realization that it had a lot going for it, but didn't touch Thunderball as far as classic Bond feel. Thunderball just drags and drags, where I feel NSNA has a much tighter pacing, but Thunderball has everything that NSNA needs. It's got the music, the look, the charm, Q, M, Moneypenny and all the quirks that make a Eon film a Bond film. This film didn't even let him have a Walther PPK.
I think the issue with Thunderball is the overly long underwater sequences. I have a much harder time focusing on the film. In fact one of the last times I watched it, I fell asleep.
I think in order to make the perfect Thunderball/NSNA, one would need to simply take Thunderball and trim the fat.
I think NSNA was neat to see Connery go at it again, but it would've been a better treat to have seen him in a different Bond plot. NSNA was made out of spite and bad blood from all involved parties.