She looks so different... The things they changed the most on her character are body proportions.
About Aloy, one looks like a plastic doll, the other one like a CGI human, like a digital version of Hannah Hoekstra
As for Ellie, she looked weird as hell in OG TLOU, like uncanny valley weird. In TLOU PT II they made her look much more like Ashley Johnson (still not like for like), so they correctly went back and changed her weird looking character (head too big, disproportionate eyes) and de-aged her a few years. But I guess this is what Norman Reedus looks like:
Your problem is not that characters look "uglier", it's that they objectively look more like human beings.