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.
Complete Monster: Zouken Matou, as per canon. Here, though, we witness his assimilation of another person's essence without the slightest trace of remorse. To top that off, Saber and Shirou are both highly unsettled by him, while Kirei has an internal monologue reflecting how much the ancient parasite disgusts him. Even True Assassin - while not actually put off by him - notes the hypocrisy and selfishrefusal to admit fault in Zouken when the old bastard complains about his situation.
Nightmare Fuel: Chapter 15 contains a scene where we see Matou Zouken assimilate an innocent's essence as he performs a Grand Theft Me upon her body. Reading it is both horrifically creepy and heartbreaking.
Shipper on Deck: Irisviel really, really wants Shirou to take care of Ilya. Make of this what you will.
Tear Jerker: In Chapter 14, Shirou is visited by the disembodied spirit of Irisviel, who softly asks him to do his best to save Ilya.
Berserker's death in Chapter 22, particularly his regret that he can't protect Ilya any longer, and as he passes she - despite being unconscious - seems to feel it, and starts to cry in her sleep.
The Scrappy: Caster Alter to some, who believe she has overstayed her welcome and survived situations she should not have.