How do girls feel about being called pretty by shy guys?

Since you're a shy guy and therefore don't go around spitting out "you're pretty" to every girl you see in an effort to get something out of her--or at least imply that you've had a lot of practice at commenting on girls' appearances--girls are likely to take your statement as more genuine, at least, compared to that of a guy who's known for his charm and charisma.

I would be absolutely flattered and think it's the cutest thing in the universe.

They love it. Most girls are pretty shy when talking to a guy they've never talked to before, if a guy they never have talked to before said that they would probably be a bit shocked and blush a little.