So far, the protagonists of this story are its biggest downside.  I don't say this to be mean... I just felt I needed to be frank with you all.  The story itself is generally interesting, as is the cast of side-characters... but both protagonists definitely leave something to be desired.

Kai

Kai's side of the story would probably be best referred to as the 'Light' side of the first part of the VN.  Why?  Because, for all the horrible things that happen during the course of his story, none of them really tarnish or dirty him personally.  That is fairly typical of a jrpg protagonist, as the 'natural hero' types tend to never really get dirtied by all the horrible things that go on around them or the people they have to kill in the course of the game.  Oh, early in the game he is a little bit more pathetic, but when he loses a comrade, it drives him to 'resolve himself' to the fight to come with the typical guilt-driven passion you see from any number of similar heroes.  To be honest, the degree to which his personality and character development is cliched is startling.  Most writers make an effort to at least move the protagonist a little away from the 'middle of the road' archetypes...

Shizuma

Shizuma is a problem for an entirely different set of reasons.  Number one is that he is a resurrection of the 'angst-driven anti-hero protagonist who is always irritated with or angry at something'.  As I've gotten into his path, I don't see this quality fading all that much.  Worse, he seems to have the fatal character flaw of being a smart idiot.  He is intelligent, but he is blind to the obvious pitfalls around him.  He fails to even consider that a certain delusion early on might be wrong, due to his obsessive personality, and he fails even more to choose an intelligent path to his goal, despite apparently being fairly smart.  A lot of this comes from the impatience that is endemic to this kind of protagonist... but that doesn't change the fact that he looks like an idiot through almost the entire first quarter of his path, despite having the typical elitist arrogance of the naturally capable ('What, you can't do that?  It's easy though.').

Edit: For those who are interested, Eternal has released an update fixing the bugs stated in the previous post, as well as rebalancing certain aspects of gameplay - the general weakness of combined mechpeople and a few other issues.  11/01/2015 1:33 AM, US Central Time