I mean, it would be less of an issue in Japan. Apparently, underage characters get panty-shots quite often there simply for the cuteness factor, and often to emphasize their lack of sexuality. but if you bring this up with people who live over here - especially people who have never heard of Lip before - they're just going to think we're a bunch of creeps. And really, Lip gets enough flack for being a "loli" (which she isn't, but you know how quick people are to assume when it comes to young Japanese-created female characters in skirts) as it is.
I never got the whole "age doesn't matter, they're a fictional character" thing. Fact of the matter is, Lip is drawn to look young, and discussion of her in the context of something that is, by our standards, typically sexual is inherently going to make me feel uncomfortable, same as it would with any young-looking character.
Frankly, if her legs didn't end up fading into a black void past the knees like what they did with Peach and Rosalina, she'd most likely wear bloomers in SSB4. It would let her keep the skirt and remain physically active in it without exposing anything inappropriate. Remember, Nintendo of the now is much more internationally focused than the Nintendo of ten or even five years ago. I'm pretty sure they're aware of what people would think if they released as SSB4 DLC a cute little girl wearing nothing below her skirt except briefs. Palutena can get away with it because, besides the whole ageless goddess thing, she's drawn as an attractive woman. Lip isn't, and can't.