I don't have any major complaints about the game's story, but I feel like they played it ultra-safe after the nonsensical disaster that was SO4. MC started out as a credible, mature, master swordsman with connections that he wasn't afraid to use. He had armies and spec ops at his back for pretty much the entire game. It didn't really feel like he or any of the main cast aside from Relia/Feria was ever in any real danger.
Probably the biggest thing that bothered me by the end is that I don't think it was never really explained why the Kronos coup faction was arming the natives and actively engaging in the Faykreedian war unless I missed something somewhere. It's kind of an integral plot point. We know the Kronos coup faction scientists were using Faykreed's native fauna (including the people) as test subjects for corruption research and that they chose to operate on Faykreed because of the whole Time Gate looking thing. But what were they actually gaining by arming the desert people and fighting the knight people? I mean, these guys are Star Trek. They don't really need a cover to abduct people. They could transport as many of them as they needed right out of their homes and the Faykreedians would never be able to find their cloaked underground base. The Knights didn't even have anything important in their territory. If anything, the Ancient Institute in Mageland was the only target of any potential value to them that they didn't already control.
I've heard a lot of complaints about the sudden, unexplained emotional development between the characters, and while I'll admit it's a little unusual that these people would be willing to throw away everything they've ever known to save a little girl they met on the road nothing else really struck me as out of place. Miki went from typical Japanese tropey "adoptive little sister" to 'omg marry me before it's too late!' after spending her whole life with MC and seeing their world get turned upside down, which is a pretty understandable reaction. As for the whole "I couldn't live without you" scene with Relia, I feel like it's fairly understandable that when you're faced with an 8(?) year old staring down an existential crisis and contemplating suicide you say whatever the fuck you need to say to make them stay alive. MC decided to become a father for this kid (probably as a result of his own issues with his emotionally distant absentee father and the subsequent loss thereof), and he went all in on it saying whatever he needed to say to support her.
Overall, this was a cast made up of adults who acted like adults which was refreshing but ultimately not particularly exciting. It's a good palate cleanser to keep the franchise alive while Tri-Ace hopefully looks at SO6.