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.
Anticlimax Boss: In Terra route, Kotarou charges into Gaia headquarters and fights one strong T-Rex. Then he discovers that Sakura Kashima is already dead. Compared to Moon Route where Sakura Kashima technically sent an army of familiars, it felt quite anticlimatic.
Bizarro Episode: In Harvest Festa, the story Strange Fantasia continues from the joke Oppai Ending.
Broken Base: Tons. Over which writer did the best job, over which writer did the worst, over what route is best/worst, whether the game is the best Key Visual has ever put out or whether it falls flat, etc.
Crowning Moment of Awesome: The part where Kotarou defeats Sakurya's giant form at the climax of Chihaya's route. Also, in general, any point at which Philosophyz is playing.
The climax of Moon where the Occult Research Society (and Yoshino) start their final battle to defend Kagari against the forces of Sakura Kashima
Carnation, Shizuru's theme is an extremely relaxing piece of music. The vocal version Love Letter also acts as a heartwarming way to finish her route.
YO-SHI-NO is one of the most hilarious songs ever. There's really no other way to describe it.
Ho Yay: A lot of Yoshino's dialogue. Lampshaded in the narration.
They have a love-hate relationship and Yoshino can be tsundere about Kotarou at times. Most importantly, Yoshino has a big crush on Kotori, who is stated by the game to have a similar personality to Kotarou (most noticeably, they both like to goof around a lot). This suggest that if they had been opposite gender, Yoshino may have very well fallen for Kotarou.
Tearjerker: The part in Terra where Kotarou is forced to kill Kagari to prevent salvation.
The Woobie: Pretty much everyone in the story qualifies as one of these considering the backstory one needs to be a superhuman/summoner aand the whole eternal war thing but the ones that stick out are Kotori who's been guarding the key in the vain hope of ressurecting her parents for about 10 years, Lucia who has been a human test subject for most of her life and Terra route Kotarou who ends up determined to save the world and ends up being forced to betray everyone he knows in the process.