They are literally the main characters of the story... You couldn't do an adaptation without them being the most prominent.
I understand the difficulty from a narrative standpoint of deciding what to do with Fujimaru, but I think the decisions of how he's been characterized in various animated entries lead to disappointing outcomes.
It's not that the ending of the fight with Tiamat is different in the show; the necessity of editing a multi-stage battle into something with a more natural arc necessitates a bit of improvisation. But the real change here is that at the last moment it takes Babylonia as a whole and turns it from being Gil's story and makes it Fujimaru's instead.
They've been kind of splitting the difference up until now, which makes sense because as a POV self-insert, Fujimaru's devoid of the kind of character depth in the game proper to make him a main character, unlike say Shirou in the F/SN visual novel. But because Babylonia's anime is so short relative to the amount of content its adapting (especially in relation to other Fate anime adapations in recent years), the necessity to add screentime to develop Fujimaru's character more or less from scratch comes at the cost of spending that time on the actual main character of Babylonia: Gilgamesh.
While Gil does technically land the final blow, the last decisive action is Fujimaru's, and I think it reveals that the people in charge of the adaptation miss the point of Gil's return. Have you ever considered
WHY Gil is a Servant? Given both his characterization as a brash, young tyrant or a wiser, confident king, neither really gives the impression he'd ever take on a role as a Servant himself, though he uses them for his own ends all the same. And yet, Gil returns as the Archer we all know and love (er hate... it's complicated) at the very end after perishing during the collapse of Uruk: to finish what he started, in death if not in life.
Babylonia in the game is meant to be the final epic of Gilgamesh, ending with his origin as a Servant, and what would prove to be the first in a new line of stories for him throughout Fate that continue to this day. It's a story about the indominable resolve of the living, played out in grandiose fashion in a war against the gods that costs Gil everything, even his freedom after death. And it even gives context to why he feels entitled to do with humanity what he pleases as a Servant when it turns out he's disappointed with how they've progressed in the millennia since his sacrifice.
I think the reason the anime didn't resonate with me during the last couple episodes is because the changes feel like they're propping up a less interesting character with a less interesting plot when the one in the game already sufficed, all because they're trying to turn Fujimaru into a proper leading man when the story didn't change enough overall to support it. I hope that the Camelot will be so focused because it's just two movies that it won't suffer from these kinds of half-baked changes that don't do anything to improve or even really live up to the source material.
