Anti-Climax Boss: Desparaiah. Kawarino poses a lot more threat and stake than her, really. She attempts to break just Cure Dream, and when that backfires, she started freaking out and one befriending by Nozomi later, she pulls a Heel–Face Turn. And that's just half the final episode.
Broken Base: Some fans who feel the franchise went downhill often blame this series in particular, due to what some perceive as a higher level of Merchandise-Driven items found throughout the series, as well as making a somewhat more traditional magical girl show with a core team of 5.
Contested Sequel: The season after the first, Yes Pretty Cure 5 Go Go, while still having some fans, is met with a bit more criticism on the whole, with many feeling it was a needless sequel with not enough connections to the original season, as well as being even more Merchandise-Driven then the first season, and is often seen as a form of Seasonal Rot for this continuity. This affected Real Life sales as well. Go Go tanked compared to the original series in terms of merchandise sales and TV ratings so badly, Toei has never made a sequel season to any continuity of the franchise since then. In a way, Fresh Pretty Cure! was made because Toei noticed how people felt tired of the core team of 5, and wanted to refresh the series afterwards. This was also because the staff behind this series was getting tired of being with the series for 5 years straight and new blood was needed, and had Fresh Pretty Cure! failed financially, the franchise would have had its plug pulled then and there.
Amongst the main team, for some reason Urara tends to be the most popular team member. She might have started the whole trend of 'Yellow Precures are probably going to be the most popular of the bunch'.
Foe Yay Shipping: Milky Rose and Anacondy, for a scene where Milky tries to engage her in combat, but Anacondy grabs her wrist and pulls her to be only a few centimeters from her face.
Girinma crosses it when he turns Urara's memento of her deceased mom into a Kowaina. Considering the importance of dreams in this series, though, it's possible that he crossed it even earlier—in the very first episode, even!—by mocking Coco's dream in a most callous fashion.
The Director of Eternal crosses it when he calls life worthless.
Shadow crosses it by killing off The Dragon who's gaining her humanity and then calling her useless and dying like a dirty traitor.
Nightmare Fuel: Kawarino's Despair Mask just look plain creepy and haunting. Not to mention every non-named Nightmare members are wearing one, and at one point, all Cures end up wearing one, to the point that Nozomi in Go!Go! used that event as 'something she doesn't want to happen again'... Well, they ain't called "Nightmare" for nothing.
And when Nozomi broke that off thanks to Coco, she dove in to her friends' mind... and found her friends first acting normal, but later revealed to have Dull Eyes of Unhappiness. Pretty chilling.
Periphery Demographic: Adult males. Then again, given that there was a "marketing" paper that listed the "main target" as 4-to-12-year-old girls and 16-to-35-year-old men, this is an arguable subversion.
Die for Our Ship: Coco and Nuts, just for being male, and before Nuts had an implied relationship with anyone; also, Crepe, once she was announced to be betrothed to Coco and thus get in the way of both the canon ship and the yaoi fangirls' favourite ship.
Squick: While Coco/Nozomi is a good deal healthier than teacher/student relationships would be in real life — Coco's an emancipated minor just posing as an adult, the teacher-to-student and Precure-to-fairy power imbalances even each other out, and there's a clear foundation of mutual respect there that's hard to find in most canon shoujo relationships even between peers — a lot of people still despise the ship and Coco himself because of the squick factor.
Tear Jerker: Shining Cure Dream and Mushiban's goodbye in Yes! Precure 5 Go! Go! Movie.
Viewer Gender Confusion: Shadow from The Movie is a Creepy Crossdresser, but no one's quite sure what he's crossdressing as. From a brief overview of the fandom, the women tend to believe he's a man, and the men tend to believe he's a woman. To wit, the voice behind Shadow is Romi Park, he/she/whatever acts and dresses flamboyantly and even kisses the Dream Collet, but has well-toned muscles on his/her/whatever's bare midriff and no boobs whatsoever. Confused yet?