Captain Ersatz: Serdic/Altrius is a pretty obvious shout out to Fate/stay night's Saber. Both are unwillingly the King of their respective country, they have the EXACT same outfit, carries a holy blade, use their swords as a Wave Motion Gun, both are arguably a one man army, although in Serdic's case he needs to level up a bit first, both are blonde, both have storyline branches that may lead them to release their Super-Powered Evil Side, and whereas Saber is really an obvious woman that everyone mistakes for a man, Serdic/Altrius is a boy that just happens to look really feminine.
Not to mention that the holy sword itself is uncannily similar to the Gran Centurio as far as its role in the plot goes...
He Who Fights Monsters: Path B. Goes from a relatively typical example of The Hero to a theocratic dictator calling himself the 'Divine Emperor,' goes from wanting to stop the token Evil Empire to wanting to conquer the Evil Empire, and starts waging a rather brutal scorched earth military campaign against them, all as a result of the aforementioned Break the Cutie from Stage 20. Needless to say, this gets him many a What the Hell, Hero? from the rest of the party.
No Name Given: It is stated at the beginning that the protagonist is an impostor, but on path A, it is later revealed that he could not even remember his own name (or perhaps have one to begin with), so Marie gave him a name.
Game Breaker: Due to being able to move and attack at the same turn (unlike mages), a lot of players see him as this. Coming early in the game, high damage and long range makes him especially ideal in attacking the enemy spell casters that have equally long range spells like Abyss Gate.
Freakiness Shame: Some other characters' comments on Alhambra's body (to start with, she does NOT like her animal features and wish them removed). But when she heard Serdic compliment on them (as he was the first out of many later), she was so touched and amused (laughing that it was the first time someone said her ears were cute) that she decided to join him.
Evil Twin: Depending on how you play the game. He joins the bad guys, and leads the city's mages against you. Gameplay wise, he can and will kill his twin brother in one hit with his own lightning. But if you manage to get Selmer to talk to him, you can get him to join you. Do note that Elmer's attack range is much higher then Selmer's movement range.
Fridge Logic tells us that after this, Serdic truly does become a theocratic dictator; not only did he pretty much conquer the Evil Empire, he married the freaking Pope, and now has the complete and total endorsement and backing of the Church.
Accidental Misnaming: Yumiluna have problems remembering people, calling Alberich several different names (which were all wrong in one way or another) among others. It's been implied that she doesn't really forget.