The thing is, for a 26 episode animation of a high-profile manga like Shingeki no Kyojin, they'll have a freaking huge budget. Naruto, on the other hand, for all its popularity is too long and bland with fillers for its own good. There's only so much you can do for an anime that'll span 500 eps long, its not reasonable to expect AoT level animation from Naruto.
On an entirely different note, if you'd watch movies like '5 centimeters per second' or 'Garden of Words', you'll be asking yourselves why AoT doesn't have that much animation quality. The reason for this is, other than the fact that AoT wasn't directed by Makoto Shinkai, is that its much easier to invest all your budget on a 60min film to make it seem near realistic than it is for a 26-ep series. Another reason is that with the length of the series, the art will get blander, atleast in the eyes of the viewer, because you've seen them alot. Backgrounds will seem over-used and ugly, when if it was just 60mins long, you'd have called these epitome of animation.