Alas, Poor Villain: Dark Precure. She spends most of the series as a stoic character who seems to exist only to dog Yuri and provide a strong opponent for the Cures. Then episode 47 reveals that she just wants to cement her place as Sabaaku's real daughter, having been made to replace Yuri. Then episode 48 gives us her death scene proper, where Sabaaku comforts his now-badly injured "other daughter" and refers to her as Yuri's sister. The vulnerability coming from the heretofore borderline-emotionless Dark as she is embraced by Sabaaku and fades away makes it even more saddening.
Art-Style Dissonance: Despite the cutesy and kiddy art, the show deals with some pretty heavy topics. Though the fact that kids actually deal with this and the show pretty much tells them that you can't always bury your feelings.
Ass Kicks You: Beautifully executed by Cure Blossom in episode six. Why she calls it a "punch" is a mystery.
Blossom seems to be fond of this, actually. And in episode 30, both she and Marine do it in a Big Damn Heroes moment.
Done again with her whole body in a later episode ("Blossom Body Punch"). She seems to think that any offensive thrust not performed via legs or magic is a "punch"...
Babies Ever After: A weird variation where the main characters themselves aren't the parents. After the final battle, we skip ahead at least a few months and learn that Tsubomi's little sister Futaba has been born.
Badass Cape: The mascots can transform into flight capes, allowing their partners to fly. Cure Moonlight can have this wihtout a mascot.
Breaking the Fourth Wall: Cobraja makes a whole herd of Desertrians from the kids who haven't done their homework. Once his army is defeated, he threatens the viewers who haven't done their homework before leaving.
Breather (Half-)Episode: The first half of episode 47. Between the defeat of Kumojacky and Cobraja and the battle versus Dark Pretty Cure and Prof. Sabaku, we see how hilarious Sunacky can be.
Easily Forgiven: The movie villain, Baron Salamander gets forgiven for all the shit he pulled, including turning his foster son into a mindless monster to reclaim his former power (never mind standard villain stuff, like immediately using said power to try burning France to cinders... which failed). While Dune in the main series gets similar forgiveness in the end, he gets to be purified to the point of becoming an essentially different entity (even if he survives), while Salamander doesn't. However, Salamander had his power source destroyed so his only way is to restart his life like a normal human instead of repeating his shits, with Olivier by his side. On the bright side, he does have a chance to change his viewpoint of "The world rejects me! I'm all alone in this world!" thanks to still having Olivier.
Sayaka in episode 3 is into soccer, and looks a lot like Rin from Yes! Pretty Cure 5. Lampshaded in episode 21 when Potpourri is scouting for the third Pretty Cure, and tells her there have been soccer-playing Cures before.
Prior to the show's premiere, some people thought Tsubomi and Erika resembled Fine and Rein, mainly because of the theme colors.
Hiroto from episode 15 looks like a young Kenshin, though the crossed scar is on the opposite cheek.
Way too many people compare Erika's older sister Momoka to Miki, right down to her being a fashion model.
Eyepatch of Power/Supernatural Gold Eyes: Dark Pretty Cure's right eye. Most of the time she fights with it closed, but her power increases dramatically whenever she opens it. As of Ep. 42, both of her eyes are gold, yet her brief appearance there seems to suggest that all three tropes still apply.
Faceless Masses: In the opening, some formless, keyhole-shaped people chase Erika and Tsubomi. Itsuki, Kanae, Nanami and a background student are the only ones with definite shapes, but the last two become formless in the next shot.
Fan Fic Magnet: Tsubomi's little sister Futaba from the finale. Quite a handful of fanfic writers and fanartist have spent some time thinking of what she would be like as a Cure.
Floral Theme Naming: Tsubomi means "flower bud", and Erika is probably named after the flower erica. Additionally, Itsuki's name means "flowering tree", foreshadowing the fact that she eventually became Cure Sunshine, and Yuri (Cure Moonlight)'s name means "lily".
Additionally, we have the mothers: Tsubomi's mom Mizuki (the "ki" part probably meaning "tree"), Erika's mom Sakura, Itsuki's mom Tsubaki ("camellia"), and Yuri's mom Haruna (the "haru" part meaning "spring"). And finally, Granny Kaoruko's name is formed with the kanji for "fragrance" and "child".
Flower Motifs: Pretty much what the entire series is based around.
Funny Background Event: Not really "background", as there was nobody in the foreground when it happened, but at one point during the first episode, a background student was shown arriving at school after getting late.
Good Eyes, Evil Eyes: Tsubomi, Erika and Itsuki are all doe-eyed to signal their status as heroines. On the other hand, Yuri's eyes start out narrow, but become larger once she regains her ability to transform into Cure Moonlight and starts bonding with the other Cures.
Go Out with a Smile: A Pretty Cure's Finishing Move causes those who get hit by it to enter a state of complete bliss; if the target is a Desertrian or one of the Desert Apostles, this is accompanied by fading away and returning to human form. Also, pretty much everyone who dies in this series goes through this.
Legacy Character: Other Pretty Cure series had hinted at this, but Heartcatch is the first to actually show it, with Tsubomi's grandmother being a former Precure. The very last shot of the series hints that a little girl bearing a striking resemblance to Tsubomi (or at least from what we've seen of her) has become a Cure herself.
Let's Get Dangerous: Tsubomi's "I've had enough!" Also, Kumojacky and Cobraja begin taking their battles with the Pretty Cures much, much more seriously after Sasorina is purified, seeking to avenge her death.
Luke, I Am Your Father: First, Kaoruko mentions never having to deal with anyone like Professor Sabaku during her tenure. Then, she mentions Yuri's father disappeared some years ago while looking for the Heart Tree. Then we find out that Dark Pretty Cure and Cure Moonlight are apparently two halves of the same whole. Sure enough, he is revealed as Yuri's father in episode 47 after his Cool Mask is sliced in two.
Merchandise-Driven: Probably the most egregious example in the franchise. The Heart Pot is a piggy bank, the Heartcatch Mirage is a jewelry box, the Shiny Tambourine lights up when spun a few times, and the Tacts have a dial that the Cures have to spin frantically to complete their spells, turning otherwise cool-looking Finishing Moves into complete Narm.
Missing Mom: Nanami (who also happens to be the star of the Mother's Day episode)'s mother has passed away.
Mundane Utility: Erika tries to use the powers of the Marine Tact to clean her room and give herself a massage in episode 39. Coffret is not amused.
Never Mess with Granny: Kaoruko Hanasaki, Tsubomi's grandmother, not only won a prominent karate tournament when younger, but was also a former Pretty Cure. Cure Flower makes a triumphant reappearance in episode 44.
Not so Above It All: Itsuki loves cute things, but she can't say so because she wants to be a great martial artist like her brother once was. To compensate, Tsubomi offers to have her join the fashion club.
Retired Badass: Kaoruko Hanasaki, AKA Cure Flower, who has fought and defeated Dune in the past. Kumojacky and Cobraja never knew what hit 'em when they temporarily forced her out of retirement in episode 44.
Coupe, her fairy partner also qualifies.
The Reveal: Why do the Desert Apostles run with their tails between their legs whenever they're in danger of being purified? It's because they're made from Heart Flowers themselves, making them functionally humanoid Desertians and subject to the same conditions.
Episode 47 also counts, with regards to Professor Sabaku's identity.
The red/magenta heart seeds are essentially Magical Girl Trans-Am.
Floral Power Fortissimo is basically a very girly Giga Drill Breaker - projectiles are thrown to hold the enemy in place, complete with a colorful background (just like the galaxy background), then the girls charge at the enemy as the finishing blow, piercing through its "heart". Then, it floats for a second, while the girls strike a pose, at which point it explodes in a mushroom cloud.
Shy Blue-Haired Girl: Averted with Erika; to make up for that, we have Tsubomi, who is a Shy Red Haired Girl.
Sixth Ranger: Cure Sunshine, whose appearance, powers, and identity — Itsuki — were revealed through leaked merchandising scans. Cure Moonlight became a Fourth Ranger in Episode 33. And then Cure Flower appears as the Zeroth Ranger in episode 44.
Spell My Name with an S: Coffret is pretty easy to figure out, but Chypre had to be vindicated by a trading card after dozens of spellings. Cobraja/Cobrager/Kobraj and Kumojaki/Kumojacky continue to be debated by fans.
Spirit Advisor: The power of the Heart Tree managed to revive Cologne's spirit and he gave Yuri a pep talk to convince her to take up the mantle of Cure Moonlight again.
Spoiler Opening: The second opening, ending, and eyecatches all feature Cure Moonlight very prominently, indicating her return in episode 33.
Storming the Castle Planet: Episode 45 kicks of an entire arc of it. Man, those Snackies can fly.
Story Breaker Power/ Game Breaker: Infinity Silhouette. A planet sized Precure, who's so powerful the main big bad, who also had grown to the size of the planet, can't even hit her. His punches literally bounce off her like they are nothing, and she literally defeats him with one punch. It's never seen again, not even in the All stars crossover movies that air after the series Infinity Silouette appears in ended, probably because of this trope.
Suicidal Cosmic Temper Tantrum: Dune. "My hatred will never disappear!" is his response after he is only barely scratched with Heartcatch Mirage. And then he turns gigantic and starts pummeling the Earth. If he wore black, he would probably outdo Kuja.
Tempting Fate: Erika's "Don't worry, if powerful enemies appear, we will smack 'em down!". Naturally enough, the very next scene has the Pretty Cures tasting a sample of Dune's real power. And then Dune reveals just what kind of monster he is...he probably wouldn't be very out of place in Halo.
Theme Naming: Along with the floral example above, all of the Desert Messengers have desert-themed, and for the Three Generals, poisonous animals-themed names: Sasorina (a play on the Japanese word for scorpion, "sasori"), Cobraja (bonus points for "ja" being a Japanese homonym for "snake"), Kumojaki (a play on the Japanese word for spider, "kumo" and his Verbal Tic), Sabaku (from the Japanese words for "desert" and "evil") and Dune (a rare English example, referring to a sand dune).
Theme Tune Cameo: The opening and 2nd ending themes are played by a cassette recorder in Episode 41. It's actually even possible, since Aya Ikeda and Mayu Kudou exist in-universe, too.
This Means War!: Desertrians destroy flowers. Cure Blossom proceeds to lay a massive smackdown on it.
Threshold Guardians: Kaoruko and that hot guy...er, Coupe-sama acted as proctors for the Pretty Cures' test to receive the Heartcatch Mirage.
Trauma Conga Line: Yuri. Before the series even begins, she loses her beloved fairy partner after he pulls a Heroic Sacrifice to save her life and suffers a crippling loss to Dark Pretty Cure. Then comes the final arc, where she is hit by a machine-gun volley of traumatic revelations and events: Sabaku is her Disappeared Dad; Dark Pretty Cure is her genetic younger sister created by her Brainwashed father specifically to kill Yuri; Dark Pretty Cure (her younger sister) dies at Yuri's hands; her father leaves Yuri to comfort the Evil Knockoff in her dying moments; and her father is murdered in front of Yuri by the Big Bad. And she still manages to hold it together enough to Save The World with nothing more than grit and The Power of Friendship. You would think that the series would give Yuri come kind of compensation or reward for all the losses she's suffered, but no.
Vitriolic Best Buds: Episode 39 reveals that this is the basic dynamic between Erika and Coffret. Coffret might not have known it yet, though.
Who Would Want to Watch Us?: In Episode 18, Tsubomi and Erika discover that one of their classmates has been drawing doujinshi of Blossom and Marine. However it's much lighter on Flanderization than most instances of this trope, and the girls even volunteer to help him ink it.
The Worf Effect: Subverted. The girls (especially Cure Sunshine) were shown to be able to hold their own against the Desert Apostles in the past, but once Cure Moonlight showed up, they were easily beaten up. Admittedly, the Apostles were stronger thanks to the Dark Bracelets, and by the end of the episode, the three of them were nearly able to cleanse them, but only after Cure Moonlight softened them up quite a bit.
Played straight with Potpourri's Deflector Shields. We first see him protect the Heart Tree from Dark Pretty Cure. In nearly every subsequent appearance, they break instantly to display how powerful the enemy's attack is.