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.
YMMV: Battle Moon Wars
Best Level Ever: Stage 29. The Type Moon protagonists finally gather their resolve and fight their alternate selves: Shiki battles Nanaya in the back alley while Akiha holds off White Len, and Shirou battles Archer within the confines of Unlimited Blade Works while Rider, Rin and Saber fight Assassin. Made more awesome by the fact that the bosses, Nanaya and Archer, must be defeated by their alternate selves: Shirou must be the one to defeat Archer and Shiki must be the one to defeat Nanaya.
Fridge Brilliance: Shirou's Nine Lives BGM is actually a very, very, very, very modified version of Emiya/Unlimited Blade Works. His rejection of his ideals not only warps his reality marble, but warps his Crowning Music of Awesome.
There's also Kohaku being Saber's Master. Given the intimacy that relationships often become in Fate/stay night it's not an unreasonable consideration.
From Phantasmoon: "If you're ever lonely, Ciel, come over and we'll play."
Scrappy Level: The final bonus stage, which can only be accessed if you collect EVERY Battle Mastery. Besides being a pain in the ass to get, the stage is also loaded with a ton of high HP enemies.
"Phantasmoon and Cutey". You start with just Phantasmoon against two mooks. Not a problem, since they can't really hurt her. But then an innocent shows up, along with Ciel and a bunch of enemies. You must protect the innocent, and the Battle Mastery is to keep her from taking any damage. You can forget getting the Battle Mastery, because the enemies go first and have no interest at all in attacking Phantasmoon or Ciel. Good luck keeping her alive, too, because even if you go all-out attacking them, the enemies will continue to ignore you and kill her. This is why everyone hates the Escort Mission concept.
Stage 34... Just... Stage 34. The first part isn't so bad, but the second part will make you scream out of frustration: There's a horde of Angra Mainyu's and you have 5 turns to escape to the left (which is very short considering how far it is), all while the Mainyu's are launching their MAP skills (Ergo, no dodging/guarding/counterattacking action, and since they are grouped together, you also have to watch the Mainyu's MAP each other, which is very long, slow, and annoying). And then there's the Battle Mastery: Defeat True Assassin, AND THEN escape. Have fun!
Those Three Bosses: Get all of the Battle Masteries and play up to Stage 53 Part Four and you get to fight against Saber Lily, Arcueid in her Phantasmoon Eclipse, and Kohaku as Magical Amber. Standing between them and you are an army of Mech-Hisui's who have 11k HP AND Defense Support, which is a very hard thing to break unless your units either have Offense Support, the Spell Fury which is limited to a few units, Combo Attacks from certain people, and Field Attacks which unfortunately are somewhat useless against certain Mech-Hisui's. Add to the fact that when you reduce a number of Mech-Hisui's, Kohaku SUMMONS MORE! All in a straight line at the back where you started from. And while you're still doing that, you still need to contend with Saber Lily's Caliburn which ALMOST reaches across the screen. Did I mention that her Caliburn is 3 squares WIDE!? And all three also have FOUR Defense Supports so you're not going to damage them that easily. AND to add insult to injury, Kohaku has a BIG FIELD ATTACK that REDUCES YOUR WILL IF YOU GET HIT AND BUFFS HER ALLIES!! Fortunately, Eclipse is easy but still has a Defense Support coming from Magical Amber so you still need to contend with her. Even if she has that Spirit Bomb move, the range is excusable and one can just simply use Alert on it. So yeah, have fun dealing with the Tohno Family Takeover Plan.
Kuu's "Premonition 2" skill is basically a middle finger towards your speedsters, and she can attack twice per turn.
The Woobie: Sacchin. She needs multiple hugs when you realize just how bad she's had it in BMW. Manipulated by Nanaya, then driven insane with bloodlust by Roa. And when she finally has Shiki's attention, Nanaya shows up and throws them both off a bridge. She gets better, though, fighting with Arcueid, Sion, and Len against the revived Tatari. Unfortunately, her next appearance is performing a Heroic Sacrifice to save Shiki from Nanaya. Unless you save her by secret requirements earlier on. Isn't it sad, Sacchin? ;_; She drops off the plot except as a battle party member; but then so does Sion.
You forgot to mention something. If you are a Satsuki fan, then you will weep tears of joy when in Haruna's badass final speech, she gives a nod to Sion and Satsuki as the vampires who fight along side the group, both of whom dropped off the face of the plot several missions back... and a main character still remembers. Later, during the ending, you see that Akiha/Kohaku took Satsuki in, allowing her to live in the basement with Len. Isn't it a little less sad than usual, Sacchin? ;_;