As you say, some of the fight scenes in Naruto move extremely well. Likewise with Samurai Champloo. The first episode of Samurai 7 looks very nice in terms of movement, and all of these are modern shows. However, that's not especially hard considering all of these examples are motion captured (even I have pulled off some stunning-looking fluid animation for Studio Trophis, merely by drawing over video footage of myself). 'Classic' anime was animated by hand, from the artist's brain. Nowadays, it's easy to take a shot of someone kicking someone else and simply trace. And trace is exactly what Naruto and others do... surely you've noticed how their proportions change drastically in the nice-looking action sequences? They suddely change from being anime proportiones, to having stumpy, real-life sized legs and arms. Either that, or they don't bother to draw at all, and just use cheap CG for the action sequences, as with much of Samurai 7 and indeed all of Macross Zero.
If you then go and look at classic action anime, like Ninja Scroll, Macross Plus, the Fist of the North Star movie from 1986, etc, you can see levels of animation easily on par with those seen in Naruto and others you mentioned. The difference is, they were all drawn without resorting to tracing a real life video sequence. And as for CG - the makers of the 100% CG fest Macross Zero have gone on record as saying they simply could not top the frame rate of 1994's Macross Plus, so they didn't even try and just used CG instead. If the makers of the show have stated that the animated action scenes of their own early show is unsurpassable in terms of frames, that kind of negates any argument in favour of modern anime's animation being better. The eye can only see so many frames per second, and you can't get better than that. The aerial dogfights in Macross Plus are utterly flawless. The final nail in the coffin is to watch the early 90's series The Guyver, and then watch last year's new version. You'll do well not to be sick all over your keyboard.
Modern anime use a lot of rotoscoping. Otaking confirmed. Now go home.