Two weeks isn't very long to start making many changes about a person. And these are appearance changes so tread with caution.
The make-up part is easy. Tell her that you love her natural look when she's not wearing make-up. Don't tell her while you're out or whatnot. Just if you're sitting around and she isn't wearing make-up say, "You are beautiful, I love seeing you natural." Or something like that.
As for the happy trail, well later on offer to shave her if you're taking a shower together. Problem solved...until it grows back.
But don't make it sound like it's a bad thing. Always feed the ego while being honest. There are always at least 2 ways to tell the truth. If you aren't in sales...good luck.