Firstly it seriously concentrates on the heroines, Fsn was more concerned about telling a flowing narrative and as a result lost the freedom of choice which made Tsukihime great, I didn't have to play Ciel's route after Arcuied's, I chose to. More to the point I got to know all the girls much better in Tsukihime.
Secondly the division between Near and far side helped define the characters and give the characters a greater sense of purpose.
Thirdly the number of heroines and important characters is larger, it helps fill out the world.
It does not really concentrate on heroines. Hisui in Hisui route is barely important, so such view is pretty narrow.
Fiction as a whole is subjective, like what you like, hate what you hate but always remember that fiction regardless of what and (especially ) in the case of fan fiction is an adaptive exercise. All the EU star wars and start trek books are technically paid fan fiction, same goes for the TMNT cartoon in the 80's and 90's, that certainly was not the original version of those characters and setting, yet still they are universally recognized by the fans as the TMNT.
Readers may have his own interpretation, but the statements of the creator takes priority. If fan fiction disregards canon facts, it's go against the letter and the spirit of the title.
Could you give us sources whether they are recognized as canon by all?
Raging over canon or slapping umbrella terms on to stories is pointless. It improves nothing. While I know I'm a minority in thinking these thought I thought it best to express them as they best explain why and how I write.
Purity of canon, even if somewhat excessive, is preferable to trampling on the author's work by introducing fanon ideas which are incoherent with his vision.