At first I was wondering why the series often talked about "miracles", particularly towards the end. Then, it hit me: "miracle" (kiseki, 奇跡) and "trails" (kiseki, 軌跡) are homonyms in Japanese. One of the recurring motifs of the series is trails of rainbow-colored piano keys. One might wonder just what Hummy referred to when the Cures got their Crescendo forms: the fact that they're miracles; or that they're about to do Suite Session Ensemble attack, which creates trails of rainbow-colored piano keys?
The names of the Cures. They're some of the primary components of music: melody, rhythm, and beat. Muse is the Odd Name Out, but she's named after the Greek Goddess of Music, which also doubles as Family Theme Naming as Mephisto and Aphrodite are named after mythical beings as well.
Many people criticized Mephisto's reasoning for wanting to fight the Pretty Cures, but this post by a livejournal user, Curekun, elaborates on this quite well:
The aim of the villains - to make everyone feel sorrow - is definitely not weak; a world without music, happiness, the will to go on, etc. would be so much easier to conquer and rule than a world filled with aspirations, determination, and hope. To sing the Melody of Sorrow is the ultimate weapon to bring down humanity's ability to resist as seen multiple times throughout the series (practically every episode.)
Ako/Cure Muse has orange-ish hair. Her parents are a blonde and a redhead and red and yellow make orange!
Noise's ability to petrify things so they won't make sound, living or not. If The Movie is any indicator, chances are the living beings who are being petrified are still conscious. And I Must Scream much? And that's only the incomplete version.