Maybe worried is the wrong term, more correctly, I want to make a good character.

Personally I think the most important part of any character is that the player relates to the character, this doesn't mean that the character must resemble a normal person, it means a normal person should understand the character and there actions.

I advice you stick with the female character, both male and female player respond well to a female character, so having more female characters than male is not so bad.

Use stereotypes, character designers often warn against this but if you use stereotype as a base and add hopes and dreams to it you will have a character that is more relatable.

Stay away from racial stereotypes till you are more advanced at character design.

I think it's a question of if you are making her intentionally unappealing or actually trying to highlight the appealing side of her that is not the looks. It will be clear you made the character so the people will need you to show them something spectacular about her other than the appearance. As long as you'll be able to do that you won't disappoint the audience.

You could look into Freya from FFIX or Yuffie from FFVII and I wish I could give you better examples of respected "ugly" female video game characters but they just usually tend to be male or masculine ones. Still any character can win the player on their side with virtues like strength, honor, courage, persistence, justice for example. From the summary you wrote on your character it sounds like you could do well with just brute strength, but I hope you show a flicker of sensitive side as well even if you hide it somewhere really deep.

I actually ended up looking up "tomboy characters" and this list is one of the things that came up: http://en.wikipedia.org/wiki/List_of_tomboys_in_fiction It isn't what the issue is about but still you could maybe look into some of the characters and for examples at how the author makes the audience like the characters despite the looks.

Writing a sex bomb super soldier like Lara Croft or Solid Snake is easy although I'm not saying these examples are the most shallow ones around. But writing a character without such an obvious shortcut does require a lot of writing to get the depth into it because that is where the beauty lies.