Many things. Basically he decided to change the story as he wants, altering many scenes, and moving lot of some important character to the sidelines and altering series canon. Do know that original game creators said that canon version of FSN is Realta Nua, so all games are based on it. Here's some of them: 1) Removing many Illya scenes, instead focusing nearly entirely on Sakura. 2) Altering Shirou's dream scene, where Sudou decided to partly adapt 18+ scene, making Rider a succubus like character,which contradicts her actual character. 3) Adapting Sakura's 18+ backstory, with lust because of worms and rape backstory, instead of her canon backstory of abuse and worm induced fever, not lust. 4) Making a fight scenes with short, simple animations and shit ton of special effects, which is lot cheaper that doing fight scenes with a lot of animations, but low amount of special effects, sure it looks cool at some point, but there a scenes where you can't actually see what's happening because of amount of special effects. 5) Impling that Saber Alter has feeling for Shirou in the third movie, whereas to VN, where there's not such thing, and other games starring Saber Alter confirm so. 6) Blatantly lying that Sudou is a fan of Fate Stay Nigh, when in the interviews when he's talking about previous routes, he makes many mistakes in basic story things, like making mistakes in Saber's and Archer's backstories, and when talking about H-scenes, he said that in Fate and UBW adaptation scriptwriters easily "gone around" H-scenes, but it will be harder to do so in HF, actually they didn't altered anything, because these scenes were rewritten in Realta Nua by Creator himself, so they just adapted what already was done, so Sudou just made these scenes because he wanted to, not because it was hard. 6) Cutting of nearly all important Illya scenes, and backstory, replacing them with Sakura scenes he made up, which were absent in the original VN. 7) Altering Zouken's backstory,abilities and his worms characteristics. 8) In second movie he replaced nearly half of actions scenes with Sakura and Shirou talking scenes, which too were not present in VN.
Many things. Basically he decided to change the story as he wants, altering many scenes, and moving lot of some important character to the sidelines and altering series canon. Do know that original game creators said that canon version of FSN is Realta Nua, so all games are based on it. Here's some of them: 1) Removing many Illya scenes, instead focusing nearly entirely on Sakura. 2) Altering Shirou's dream scene, where Sudou decided to partly adapt 18+ scene, making Rider a succubus like character,which contradicts her actual character. 3) Adapting Sakura's 18+ backstory, with lust because of worms and rape backstory, instead of her canon backstory of abuse and worm induced fever, not lust. 4) Making a fight scenes with short, simple animations and shit ton of special effects, which is lot cheaper that doing fight scenes with a lot of animations, but low amount of special effects, sure it looks cool at some point, but there a scenes where you can't actually see what's happening because of amount of special effects. 5) Impling that Saber Alter has feeling for Shirou in the third movie, whereas to VN, where there's not such thing, and other games starring Saber Alter confirm so. 6) Blatantly lying that Sudou is a fan of Fate Stay Nigh, when in the interviews when he's talking about previous routes, he makes many mistakes in basic story things, like making mistakes in Saber's and Archer's backstories, and when talking about H-scenes, he said that in Fate and UBW adaptation scriptwriters easily "gone around" H-scenes, but it will be harder to do so in HF, actually they didn't altered anything, because these scenes were rewritten in Realta Nua by Creator himself, so they just adapted what already was done, so Sudou just made these scenes because he wanted to, not because it was hard. 6) Cutting of nearly all important Illya scenes, and backstory, replacing them with Sakura scenes he made up, which were absent in the original VN. 7) Altering Zouken's backstory,abilities and his worms characteristics. 8) In second movie he replaced nearly half of actions scenes with Sakura and Shirou talking scenes, which too were not present in VN.
obviously Sakura's route will have many cuts because this route is made in movies, unfortunately it's not possible to faithfully adapt everything in 3 movies even if it was in episodes it would have many cuts, and the fate routes in VN have a lot of dialogue it's natural that have cuts to be dynamic for the viewer even more in a movie, Fate is a game eroge the excuse they gave is that the HF route has many scenes 18+ so this route had to be adapted in movies because it couldn't be adapted in anime for tv, but all VN routes have scenes like this so we know that it was not because of this that it was adapted into movies in the end I understand what you mean by wanting everything to be faithfully adapted without cuts but it would be impossible even if it was made in anime, as a fan who played the VN it didn't bother me the cuts in HF the adaptation was impeccable for the plot of the film, the only thing that bothers me in the adaptation of the universe of fate to anime is the route of Saber, from rest FZ, UBW, and HF made by ufotable are impeccable the HF animation in the fight scenes are perfect as always the special effects didn't bother me at all, and they are not simple fight scenes if it were simple every studio would be able to do like ufotable, I think you watched the HF fight with the TV closed lol.