I agree that the Fate route is very bad but trying to make it better by introducing plot points from the UBW and HF route like DEEN did is not how the right way to improve it.
As I said, poor amalgamation. The anime sure has its problems, but since I judge them individually the anime gets more points in my book, simply b/c it manages to capture fundamental aspects like themes and characters well enough to complement the story (albeit loosely at certain points).
The VN is meant to be experienced by reading all three routes to fully grasp everything that it touches upon, but I'm personally not a fan of such a method and I don't think removing core aspects within a narrative and simply label something as "read / watch the next entry to get further exposition on this matter" as a justification. If a character is missing vital characterization, or a narrative thread is unexplained within the narrative, then that is bad writing. I'm not experienced with VN, so maybe this is a norm with entries that have multiple paths which requires one to experience all paths to make the story "whole", though I don't judge individual stories that way.