Doesn't matter if it's not finished, there is no redeeming this fic.
Alright, let me start right off the bat by saying that, even though it's not yet finished, this entire fic's premise is to take likable characters and make them villains. If you're going to do that, then you've failed as a fanfic writer before you've even begun.
In the series proper, Twilight Sparkle has always taken time to put a lot of thought into responding to new and unfamiliar situations, but in this story, she takes a cursory glance at the human race and then writes them off as the bad guys, going so far as to provoke all-out war.
While it would make sense that she wouldn't necessarily make the best judgment in such a situation, the fact that Princess Celestia actually stands by this statement is utterly baffling.
Did the author somehow miss that learning to understand, and more importantly accept
others' differences is the central theme of the actual show?
Twilight has always been portrayed as a character who would at least try
to be open-minded in an unfamiliar circumstance, and while she may not necessarily succeed, having her make a broad generalization for an entire species is not something that she would do.
And then Princess Celestia, who's been shown in canon to put as much effort as possible into establishing some sort of mutual understanding, goes against everything she's ever been shown to stand for by continuing this position. I don't believe it for one second.
The story itself also draws uncomfortable parallels to World War II, and it appears that the Equestrians for Humans organization is based off of the White Rose, a resistance group against Nazi Germany.
So, the Equestrians are basically Nazis now. It doesn't matter where the fic goes from here or if they learn their lesson, this is a premise that utterly fails to begin with.
As per Godwins Law
, the discussion ends here.