Gotta say, I've always found the whole "Good Uncle"/"Bad Uncle" thing ironic, because either way, Sensei is still a horrible uncle. Just Fingering Ami makes both a little happier. While not Fingering Ami doesn't.
Basically "Bad Uncle" has Ami think Sensei is the "Best Uncle":
While "Good Uncle" has her well, as she puts it:
And not exactly "happy":
Not sure if it'll actually "matter" in the end, but if any of the variations would, it's probably this one (and Sara's probably in retrospect). Still, I'm definitely interested in how things will be now, after what happened to Ami.
The game does at least imply it'll end badly if you don't fuck Ami:
But I think it'll depend on what's actually going on. Might just get cussed out by the Xoanon. Or the other girls start not coming back from resets.