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.
Fashion-Victim Villain: Between the Science Guild's pear-shaped clown outfits, Kou and Madoka's enormous nipple-plugs, and Ryousuke's man-thong and see-through body-stocking, the Order of the Glittering Crux has something for everyone.
Kanako: Startlingly attractive? Check. Large, bouncy breasts? Check. No-nonsense personality (at least in her Crux form)? Check. Incredibly strong with a straight punch that can knock almost anyone out in one hit? Check, check, and another check. Outfit strangely resembling bondage gear, complete with Nice Hat? You guessed it: check. A WHIP? DING DING DING.
Foe Yay: Takuto and every female Glittering Crux member introduced so far with the exceptions of Keito and Undine, as well as Sugata and Head.
Freud Was Right: Episode 9. Sugata tells Takuto to be careful because his kendo sword is a bit longer, while holding it out in front of Takuto. Generally, much of the show could qualify, as it's about a group of teenagers trying to "break the seals" of "pure maidens" to unleash their hidden powers.
Madoka's "3.5" fusion with Hegent in episode 21 makes Ayingott seem cute and cuddly by comparison. Uncanny Valley combined with the most blatantly psychotic character in the series? No thank you.
OT 3: Since listing specific examples would take up most of the page, let's just say that this show has a lot of Takuto/Wako/Sugata Ship Tease and leave it at that.
The end of the series points towards this, especially with Wako's line of "You don't know how much it hurts to deeply love two people at once.". Neither Takuto nor Sugata seem to mind.
The Scrappy: Madoka and Kou are two of the least liked characters in the anime, mostly because they show up out of nowhere in the middle of the series, aren't really developed at all, and spend about 4 episodes stealing away screentime from other characters that could have used the development.
Space Whale Aesop: Use a condom, otherwise, when having an affair with a girl you are just going to abandon, you will more than likely engender the one person capable of defeating you and ruin your evil plans.
Squick: Whatever Keito was doing to Sugata at the end of Episode 18 required her to be naked and him to be unconscious and unaware of her presence... and she was given the go-ahead by his own family. Even if we don't assume the worst, the vibes given off by that scene were very unsettling indeed.
The infamous Gag Sub "Please do not imitate rapists" didn't help.
What Do You Mean, It's Not Symbolic?: Not the world's deepest symbolism, but every Cybody is named after a letter of the Phoenician alphabet, and each letter of the Phoenician alphabet has a name whose meaning informs the abilities of the Cybody and its controller. Alf is "ox" (piloted by Raging Bull), tet is "wheel" (Speed Kid), pe is "mouth" (Scarlet Kiss), nun is "fish" (as in "Little Fish"), samekh is "pillar," ayin is "eye," etc. etc. You could figure out who will control what based on their codename (rosh means "Head," gee, I wonder who will pilot that?), as well as how many Cybodies there will likely be (22), which was confirmed in series.
Matthew 19:24 "It is easier for a camel to pass through the eye of a needle than for a rich man to enter the kingdom of God". Now who was it who stopped Camel Star from advancing to the fourth phase?
Sugata's Glittering Crux outfit. And I'm not even touching on those peacock feathers either.
The Woobie: It's a tossup as to whose life sucks more: Simone, whose father abandoned her and her mother for a girl one year older than her; Mizuno, who had all her romantic dreams crushed in a single day by the return of her mother, an eavesdrop on Takuto, and her destiny as a Maiden; Sora, Takuto's mom who was driven by the unresponsiveness of her fiancee to a man who did not love her; or Ryousuke Sora's fiancee, who loved her all along, and who blinded himself when he witnessed her infidelity through his first phase.