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and using Mordred gives character development to Saber (assuming we don't change hercules with Lancelot) provide her character development is important.
I guess that could be a thing, personally i didn't see it affecting shirou.
Ayako and Shinji
Kirei could be the impetus for shinji getting a servant assassin.
and ayako getting caster won't affect the balance of the story, not in a major way as caster will be weaker