I think the Сharacter Сreator in all ME games was very very poor. Too few hairstyles, so few acceptable eyes, mouths, noses, and those was almost all ugly and weird. Let's hope that in ME-Next we will get much more diversity and possibility to make our hero beautiful and handsome. OK, not necessary beautiful, just nice. 
Well, its not like Femshep is supposed to look like some supermodel walking around in high heels and wearing a mini skirt.
Overall, I think the series did a pretty good job with how you can change your characters appearance. I seem to remember a FemShep Fan Thread around here (back in the ME2 days) where people did some really amazing work. As for ME3, I did not see any of that kind of stuff - probably because I hated the story so much that I never cared for making my Male Shep look like me. I just used the Sheploo default and rolled with it. The more that I can distance myself from it, the better.
What would be nice though, is to have the ability to import from one game to the next - and have it work. I'm not a programmer or anything, so I have no idea how much work that would take as we switched game engines through the series.
I feel like they did their best - at least as far as faces go.