(Spoilers for Rewrite, particularly for the Moon route. If you have not completely read Rewrite, please do yourself a favor and get to reading.)
By no means would I call Rewrite “perfect”. One of the Rewrite’s greatest flaws is its lack of coherence between its routes. It’s bound to happen when a work has multiple authors: throughout its routes there are contradictory scenes, plot devices and characters left unused, thrown away, or just rendered unimportant in the grand scheme of the work. Rewrite, as a whole, is a chimeric mammoth of ideas which don’t quite work together.
So what is it that keeps Rewrite from being a complete mess?