Emiya, Einbern and Gilgamesh all found out that something is wrong with Kotomine. It was never about "he became that", it was about "he never found out what he was all along". He was a dark reflect of Shirou. And before you fault Urobuchi for Kotomine and what he was, it was Nasu who decided this for Kotomine.
All Gen ever needed was to write Kotomine's start of darkness and awakening to his true nature, and outline the events that eventually led to it. Why Gen instead of Nasu? Possibly because his previous works at Nitro+ have shown that he is one of those able to talk about the inhumanity of humans (like in Saya no Uta) and the downfall of people in a compelling way.
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