Ass Pull: While it turns into a Moment of Awesome pretty quickly, it's hard to deny that the shy Shrinking Violet Riko having been Liesel in disguise for the entire game is completely out of nowhere.
Though it could also be Fridge Brilliance. Besides, if Shizuka and Arata's mother were incognito for years, that means Liesel being a sleeper agent is not out of the question, and since it's implied she's been on Earth for awhile, she already has a marked advantage due to having already sussed out the terrain of the battlefield.
There's a subtle metagame hint if you notice that unlike the other schoolgirls, Riko reacts not to Chris, but Arata. This means little in-character - but due to the game revolving around Arata, it implies that Riko might be more important than expected.
Since Arata is the viewpoint character, it is reasonable to have surprises out of nowhere, since that's what they would be for Arata.
Audience-Alienating Ending: Arata and Chris end up together, no matter what your choices. That's not the problem, it's that they're both Kissing Cousins and paternal half-siblings. While it's true incest was once rather commonplace in royal families (and sibling incest rarer but far from unknown), it's not something most players want forced on them.
Awesome Music: Battlefield of Steel is the default fight music, but it never seems to get old, no matter how many times you hear it. Daybreak is the song that plays during a few of the story's CMOA's.
The Danza: You wouldn't have guessed that Shizuka herself is voiced by Shizuka Itō, if it weren't for the fact that she used her eroge name Rina Misaki.
Fetish Retardant: The first sex scene between Arata and Chris can come off as this. They're driven nearly insane with lust by a side effect they weren't aware of, and their bodies just basically go at it without being able to stop themselves.
Fridge Logic: Chris was raised almost in isolation in the palace, yet he somehow manages to be a great basketball player.
Fridge Brilliance: Chris spent most of her life trying to deny she was a girl thanks to her desire to become Emperor. In addition to the situation with Shizuka, Chris also becomes embarrassed like a boy would when she accidentally walks in on Nodoka and her classmates changing for gym; usually a girl would have no more reaction to the sight of girls in their bras and panties than a guy would have at the sight of boys in briefs or boxers. It's possible Chris might have tried so hard to think and act like a boy that she started getting some "boy desires." Or, y'know, Chris is just bi.
Moe: Regardless of the seriousness of the story; being an Eroge it's still in there, all though not many would have expected it to come from Liesel.
Padding: The writers took a leaf out of Nasu's book; the fight scenes definitely don't use one word when seven would do.
The Scrappy: April spends much of the early story being only mildly funny comic relief, but after the big Wham Episode she becomes what seems like the most loyal and enthusiastic of the Big Bad's henchpeople, enthusiastically mocking and taunting the team while engaging in heinous actions. Only the revelation that she's almost certainly a goddess orchestrating events to destroy him once and for all saves her from outright Hate Sink territory, and even then, her actions come across as too aloof to the characters' suffering to ignore.
Squick: Arata and Chris end up together, regardless of your choices. Not only are they Kissing Cousins (their mothers were sisters), but they're half-siblings. This is a level of incest even most H-games would find questionable.
Woolseyism: At one point when talking to Suzushiro as Iris, Arata/Chris use 'ore,' which is an absurd pronoun for someone like Iris to use. English can't do that. Instead, they change it to make it as though instead of slipping with what pronoun they're using, they accidentally refer to themselves in the plural with 'we.'
is the default fight music, but it never seems to get old, no matter how many times you hear it. Daybreak