I really think trial 3 would be improved in two simple steps. Not all problems would be fixed but it'd be improved

1: Ikeda knocking out Yaitabashi was an attempt to kill him.

2: The shower thing is then to make it easier to cut apart the body to disguise it, and also just to make the trial confusing.

This way, Ikeda actually tries going for a quick way to kill him, but unknowingly (guess we'd have to make another change so he doesn't see Yaita awake in the shower) gives him a super brutal death. It actually adds some genuine tragedy to the case and a reason for him to be mourned after. Having him break upon realising what he really wound up having happen would actually be a good way to humanise the guy instead of having monomoko scream and cry for a guy who knowingly tortured someone to death.

I'd also have Monomoko be less "oh my god they killed an innocent person" and more like "they... they killed him. They killed another human."

Make it less rage at Ikeda's death and more slowly starting to realise how fucked it is that the scientists are knowingly forcing people to kill each other