Geeky-ness aside, I think I figured out why Man Of Action changed her look the way they did. In the first season, young Gwen met her future self in the episode "Ben 10,000". Aside from obvious developments and enhanced magic skill, there was little difference between the older and younger versions. In the last episode, "Ben again", 16 year-old Gwen saw her 11 year-old self and, aside from the glasses and skirt she now wears, there was - once again - little difference between them. This is the case both times because, I think, because it was intended as a way to prevent the past Gwens from asking to many questions about the future. But that's just my theory.
Don't have a theory for the freckles. But they looked better on her before her hair got cut. Eh, what are ya gonna do?