Makoto has the hots for Jin but Tsubaki I doubt it, I think she just misses him because they were close when very young it seems.
And as for his character, I understand what you mean Xemnas but I think his route is logical. I mean it makes sense, he was confused as a child: having dependency and jealousy issues, no parents unless he was close to Nine's sister, and then out of no where attacks Ragna whom he has been vying for attention from for a long time. So he tries to work hard to distract himself from said memories and hopefully attract people he'll be able to get along with since he's bad with people. And as for his cold demeanor, well the book says itself he values nothing so why should he be nice if he doesn't know the value of things.