I think that was the point. As many have alluded to (including myself) this film pretty much assumes you know the HF arc or at least most of the rest of Stay/Night. Characters like Saber, Rin, Archer, Lancer, Kojirou, Caster, Kuzuki, etc are all explored more in the other two routes. HF is mostly about Shirou, Sakura, Shinji, Rider and Illya, so it's not really too much of a surprise to see it focusing heavily on them. (Minus the later two so far for this film though, so really just Sakura and Shirou here)
tl;dr - presage flower knows what it's presenting and does what it can to let you know who the story is focused on. I personally don't think it's a bad approach, but it's not one that everyone is going to agree with either, as we can see. Again though, we're only seeing part of the presentation now with the first film. ufotable changed some things here and there and picked where to halt each point in the story for the films, so I'd say let's try not to judge too harshly until we have the completed product - even if it is at least two years away, I think. :|