It takes a little practice but I think I've gotten better at creating halfway decent faces. Something you have to look out for is you can have a face that looks great in ME1 but for some reason doesn't import so well into ME2. Case is point, my soldier femShep Jade (that I liked to before.) All through ME1 she looked fine but in ME2 her cheekbones suddenly became razor sharp and yes, a chronic case of duck lips.
I don't think there's any real change with the imported geometry, it's just that the upgraded graphics engine highlights faults that aren't as obvious is ME1. It's so bad I went back and recreated Jade's face exactly as is was then using that as a base, tweaked it to de-emphasise the cheeks and lips while still keeping her recognisably the same person.
Another thing is where you think you have one you're happy with but after a couple hours gameplay you get to some cutscene that uses a weird angle, light or odd facial expression and suddenly it all looks wrong.
I found it's even worse with maleSheps as I've never been able to get a face that looks even close to what I'd like and even then, for some reason I can never get used to Meer's voice coming out of anything other then the default face. partly why I stick almost exclusively to femSheps.
[EDIT]
OK, since as of this week I now have a femShep for each class, I threw this together just for the hell of it.

...And yes, I made Alyxa a little ugly on purpose.