I think the character should be attractive in one way or another. I mean it definitely shouldn't be perfect. First of all it is impossible to create a character loved by absolutely everyone. Second, trying to do this, you are likely to get Mary Sue instead of a nice character.
You've said the right thing. The readers should emphasize the character. So he or she doesn't have to be perfect. I guess "average but special in some way" would be a better description.
The guy who didn't like the freckles is just one of those who can't shut up and find it most important to share their opinion nobody asked for. And he should be ignored, because his opinion doesn't matter. You are the author and you know better how your characters should look and act. If you keep reacting on such "experts" you may easily fail your story.
When I started my own comics, there were some people who always complaint about anything just to complain. One said the main pairing developed to slow, others said the same pairing developed too fast. They also complained the main character (male) looked like a girl with his long hair, etc, etc.
People complain about almost every detail. But when I see lots of likes and other loving comments, I understand that those people are either haters, or just silly guys who always "know how to make it better". They don't. It's not their story, not their characters, they know nothing about your plans.
I don't mean you should absolutely ignore any critique. But in case you need an advice, you can ask for it. You don't need it every minute from some anonymous mean haters. And you don't have to change any tiny detail each time some noname doesn't like it