As a previous friend brought up (whom I now agree with), Spirited Away isn't as amazing as other Miyazaki films. I'd say the general consensus is a tad overrated, and the likeliness is because that is probably one of their first Miyazaki films they've ever seen thanks to it making it to North America. It has Mononoke to thank for that publicity outside Japan. Animation is superb undeniably, but plot-wise, there's way more to other films than Spirited Away. Examples include Grave of the Fireflies, Princess Mononoke, and Nausicaa.
Call those one of the better anime movies.
Madoka Rebellion is in itself a stupendous anime in general. I haven't watched other recent movies to make a comparison in that regard, but I would imagine them not matching Rebellion though.
edit: Actually, I've seen Garden of Words (Makoto Shinkai). That one was great for the most part, except it seemed like the climax got rushed for some odd reason. Because of that, for the purpose of this thread, Rebellion trumps Garden of Words.