In the Grail Dialogues scene, Saber's entire motivation was wanting to rule better. She then comes across two other kings (who she could not have met while she was alive) who tell her that her entire way of ruling was wrong. Whether their ways were really better is beside the point; these people were just as great as she was, and had faced all the same problems, yet they had no regrets.
It wasn't because they were men - no other two men could have affected Saber that way - it was because they were kings. It's hard to find world-famous kings who aren't men, and more gender-bending wouldn't work here (besides being weird), since a "king of the people" wouldn't try to hide their gender.
That scene had important character development for Saber, and great analysis of what it means to be a hero in different eras, but there's no way to write it that doesn't have two men upsetting a woman.
On Saber crumbling before Berserker, the whole point of his story was that
he crumbled before
her, to the point where his mind was completely destroyed. He doesn't even question her ideals directly, Saber gets upset because she's seeing her closest friend reduced to a mad beast because of her actions. That scene was about Saber, not Berserker; Berserker's character is defined solely by how he relates to Saber. And showing her easily fighting off Berserker in that scene (while the latter was using his full power and wielding an anti-dragon Noble Phantasm) would cheapen the drama.
Rider didn't want Saber as a prize (and was rather disturbed that Gil did), he just wanted to slap that dumb martyr complex out of her. He did ask her to join his army, but he asked every Servant that.
As for Lancer not dying though any fault of his own, doesn't that make things worse? It means that the universe is completely unjust; also, Lancer is a sore loser in his death scene, screaming curses at the world because one person betrayed him. Same thing goes for Kariya, who is the most incompetent character in the story and only manages to stumble around by having a hax Servant. I'd say his death is the most undignified and pathetic of anyone in the series, his corpse sliding into a pit of worms as the person he'd tried to save calls him an idiot.
I'd say the strangling scenes are meant to be disturbing. And honestly, there's far worse in the Nasuverse.
Ryuunosuke's death was a bit less peaceful in the LN (IIRC his head exploded), but they had to tone it down for broadcast.
To "there is only one female Servant", I would counter that Saber drives the plot more than any other Servant, with the others' motivations somehow being tied back to her (Lancer wants to fight her, Rider wants to save her, Caster wants to "save" her, Berserker wants her to save him, Gilgamesh just wants her). Saber fails at things because her story is a tragedy.
I should note that Assassin has even less personality than Maia.