well... Default FemShep and Ashley are plain ugly in ME3. But it was mostly due to the texture and the bad makeup they pile on them. Like someone attempting My Boyfriend Does My Makeup...
Jack actually have the same makeup theme as Default FemShep but it work for Jack because her features is feminine (like Natalie Portman) while DefaultFemShep have strong eyebrows, strong facial structure and strong lips which makes her look rather awful with goth makeup. Ashley and Yvonne Strahovski both have strong facial features which is why minimal makeup suits them the most. Liara did have makeup issues too, its like someone smudge a crayon eyeliner on her, making her look panda-eyed.
There's nothing wrong with your kick ass CGI character to wear makeup but as in real life, makeup are supposed to make you feel good and look good. I like my FemShep with heavy eyeliner and smokey eyes because in real life, I do exactly that and its pretty low maintenance too. FemShep doesn't look like she care about touching up. She's more like a lipbalm person and heavy eye makeup is practical for someone with sleep-deprivation but need to be outdoors all the time and don't like it when people say "you look tired today".
Besides, VanderlooShep is always prettier than everyone. He's a supermodel.