I always thought NGNL’s ending to be pleasantly catchy and uplifting, but a bit syrupy sweet. To suddenly yank Sora out of it, leaving Shiro alone, futz with the audio, and dull the colors…that was an awesome subversion of expectations. This clip I just found nicely compares the two versions.
I’m most reminded of two other excellent “remixes” of OPs: Umi Monogatari’s “Dark OP”, one of the saddest and most beautiful OPs ever, IMO (especially in context with the normal one), and Angel Beats! “Rock” OP sung by Yui (LiSA).