Well, you said if even I disagree with you, you wanted to hear it, so..........
I don't believe a 13 yo girl needs a bra and panty set from VS, where they focus on unrealistic body images, and being sexy. A 13 yo does not need to be sexy, despite what the media tell us. I think our teenaged young women need to feel that their body is perfect, just the way God made them. If they don't have large breasts, there is nothing wrong with that, and they shouldn't be taught to pad them! Telling a girl that she can just wear a padded bra is definitely giving her the message that what she has is not enough. I don't think that is what you want to tell your niece, because you said you want her to feel good about her body. Plus, showing teen girls how to be "sexy" could lead to them having to make choices that they are not mature enough to make yet.
IMO, I think it is her mom's place to do THIS part with her, or at least be present at the time. But if you are going to do it, I think you should take her to Nordie's or Dillard's, or as Sarah suggested, the place in Hyde Park. Let her pick out a pretty or cute bra and panty set that does not focus on being sexy. Let her know how important it is to always be fitted for her bras, so that she is wearing the right size. (This, of course, if she is not embarassed about someone fitting her in the first place.)
As for make-up.... again, I think it's important to let her know she is beautiful as she is, and that her intelligence, strength, humor, resilience, kindness, and grace are much more important than putting on make-up. I personally think mascara and lipstick are enough at the age of 13. (Heck, that's all I do NOW!)
Make-up is not good for our skin, anyway. It would be more beneficial for her if you taught her about good skin care (and good skin care products). Teach her how important it is to NEVER go to bed with make-up on, and to wear sun block EVERY day, and use eye cream under her eyes, and moisturizer on her face. She may not totally understand now, but when she's 35, and still has no wrinkles, she will thank you! :)
Manicures, pedicures, getting hair styled - all very fun and girly, and focus on caring for one's appearance, not changing it.
One more idea..........Joining a weekly Jazzercise type class or kick boxing or such, would be fun to do together, and teach her the importance of exercising, and staying fit and healthy. It would also help her be strong and confident.
Have a good day!
J.