These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The "Nissan Combination" (Nao and Akane) is also highly widespread and pretty much rivals Nao/Reika in popularity when it comes to pixiv fanart.
In the non-yuri side there's Miyuki and Wolfrun, which acquired quite a bit of fanart at pixiv as soon as the first episode aired.
Foe Yay Shipping: A lot of people on pixiv like pairing up each of the Cures with the villain they fought in episode 23. note Meaning Sunny/Wolfrun, Peace/Akaoni, March/Majorina, and particularly Beauty/Joker. Of course, this means Miyuki is left over—fanartists are split between keeping her single or having her and Sunny compete for Wolfrun.;
Idiot Plot: Episode 14. Ever hear of cellphones, girls?
Internet Backdraft: The massive rumors about a Saban Brands show being created called "Gangnam Girls". After they found out that the plot was extremely similar to Smile's, the fandom assumed Saban might have gotten the rights to Smile and got up in arms because 1) they changed the title, when Smile Pretty Cure is already an English title name and 2) giving a Korean name to describe a Japanese anime is a little on the offensive side.
It's been found that Saban couldn't trademark "Gangnam Girls" and they may be changing the title to "Glitter Force". Which is somewhat better.
Launcher of a Thousand Ships: Nao Midorikawa. She is mostly shipped with Reika and Akane, but after Episode 18, Nao/Yayoi fanart began to surface, and after Episode 23, she gets shipped with the Beautiful All Along Majorina. And then there's Episode 25, which ignited more Nao/Akane shippers.
The fandom tends to portray Reika as a Yandere after the shot of her watching the girls from behind a door reached Memetic Mutation levels. Nao/Akane shippers from Pixiv playfully use this trope on her. Minor classmate Hiroko Kanemoto also gets this treatment combined with Stalker with a Crush.
Moe: The fandom thinks of Yayoi as this, if the large amount of fanart she got on Pixiv after the first website update is anything to go by.
Mood Whiplash: In a complete coincidence, in the 13rd episode ending, news flash appear about a bus accident in Japan which costed 7 lives and 38 injured men. All while the screen shows the Precures happily dancing and the aesop of the episode is 'bad luck will go away if you smile'. Errr... yikes?
Moral Event Horizon: While he doesn't actually cross it by virtue of being Brainwashed and Crazy, Straw NihilistJerkass Wolfrun at the very least proves himself to be a Not-So-Harmless Villain in episode 40 when he tries to kill Miyuki as part of a vendetta against Akane and everything she cares about. Smashing the precious charm her friends made for her earlier in the episode was at worst a slightly extreme example of Kick the Dog even for him, but this is the first time a Cure has ever found herself in mortal peril.
Narm Charm: The characters are almost self-aware that they are supposed to be larger-than-life characters in a fairytale, leading to this trope. Especially Miyuki.
The Producer Thinks of Everything: A minor example, in the first ending's Cure Peace variation where she face plants, her face is red afterwards. This is the only time this happens.
Visual Effects of Awesome: Aside from the series animation being pretty good overall, the first ending's CG animation is GORGEOUS, rivaling big-budget movies. The animated movements are also amazingly lifelike.