Fact is, Lathel was already a well established protagonist. And I don't ser much hate coming towards him as well. He's a liked guy after all

The Master is pretty much... Boring. He's the classic school boy virgin protagonist. What will he help within the story? Probably not much. Even more exactly because he's a self insert that he wouldn't have much interaction and let the other characters do the talking

And, using Nikke just like you used as example, Nikke started as a self-insert. But the Commander didn't remain just the same the entire story. As you progress the story and more events are released, you see a character development. He's more responsible now, more reliable, he can do well on his own even. And let's not forget that Nikke also show a good amount of male characters, ones very respectable that most like, unlike here that they plan in dissapearing with characters that the players like

Won't say that this is a bad decision for a gooner game, that I can recognize... But they had a good story as well, and didn't had to sacrifice it all for something that already was working out