Atropos shouldn't have died (although they did give us a happy ending in which she lived, she should've had more of a role in the plot).
Element of theatrical writing, when a character has served its purposes, they're killed off. Personally, I think that particular arc works out as is because it does close the mystery that was Robo before Chrono & com. found him, gives greater insight into how this future is all kinds of not-good, and adds some tension and drama. All of which is particularly impressive and sufficient to the plot particularly since the greatest driving force in the game is to change this future from happening, so its not so much necessary to flesh it out anymore when its done very well with what it needed to do.
Personally, I've change some elements to the oceanic palace incident as Schala's 'rewritten' fate really doesn't fit. As upsetting as it may be to many, I'd rather her be directly killed off between the palace transitions then just magically flung to an obscurity in time-space.
Outside of that, at this point the best 'improvement' CT can get is a story sequel that continues from Triggers perspective. No more