Tentative recc for
Dragonic Fate Works. It's a crossover between FSN and HSDxD (there are several).
It did some things I really liked:
1) It put thought and effort into explaining a mechanism for the crossover.
2) The bad guy with a Sealing Designation was surprisingly three-dimensional. (Although I think his power-set suffers from Too Many Unicorns, ie, there are too many spells without a binding theme).
3) There is conflict between Shirou and the HSDxD cast that's based on personality friction rather than just straight-up fighting.
Now, having said that, there are some painful things picked up from other fanfics I would have advised the author changed (eg, Shirou swears "by the Root" a few times, and he's got "Wrought Iron" in a nickname somewhere, and I think the author doesn't understand what a "Type" is). Also, some of the characterization is, let's sum up as, heavy-handed.
But I was willing to give all the flaws a pass, fundamentally because "think hard about HOW you're crossing over the two fandoms" is a drum I bang a lot, and this guy is reading the same sheet music.