This story was absolutely wonderful. Kiri and Kiritsugu badassness in the initial chapters was incredibly pant-jizzing. And the pleasant surprise of involving the protagonists of Tsukihime and Fate brought a smile to my lips. Their interactions are smart, witty and funny, and their combined might is something to seriously fear.
And I second what was said before that Satsujinki Shiki is a much more appeasing character. The silence coupled with those short breaks he spares for wit and surprisingly sarcastic no-nonsense work really well. Shirou... well, I never did connect much to his character, mostly because even in this kind of situations it still seems like he has worries that are completly out of the paradigm the situation requires. He also manages to be surprisingly pessimistic sometimes. Are you seriously thinking about the people who can't be saved because they were twisted already as opposed to rejoicing to the ones you saved?
Though, Shiki and Shirou interaction is brilliant.
I still find it funny how the Type-Moon universe is filled with such HAX protagonists sometimes that the best way to bring out their badassery is to make characters that are even more HAX, in a way.