In my experience if a beautiful female sim has a son who looks like her he'll look weird, and when a pretty male has a daughter who takes after him she'll also look weird. So when I'm creating sims I also check what they'd look like if they were the opposite gender.
But I also feel bad changing their genetics, I do allow myself to give them chins or a bit of a jawline if they don't have any at all or make that huge nose a bit smaller without changing their nose "type" itself (I mean not selecting a new nose from the menu). But otherwise I try to play around with finding the right eyebrows and hair for their face. I don't change their haircolor however as my sims usually have natural haircolors anyway. Sometimes (CC) makeup can help!
So I'd say I try to keep any changes very minimal.
