For "well, aren't you cute" we need context.
"Cute" does not always mean pretty, attractive, pleasant, etc. Babies can be cute, boys and girls can be cute, dresses and blouses can be cute, and even rooms and houses can be cute.
(a) Bill - I want to you meet my five year old daughter.
Jack - Well, aren't you cute! You look just like your mom.
(b) I love your Mini Cooper. It is so cute.
"Cute" can also mean witty, clever, etc. (Espirituoso, intelegente, etc.) But it usually used in a very negative, critical manner.
1-The professor thinks he is so cute. He knew we were going to the game in New York but he gave us lots of homework that is due on Monday.
2-Stop acting cute with your sister or I will tell your father! (Behave!)
3-Don't get cute with me! I know when you are lying. (Don't be evasive. Don't lie to me.)
4-I told you to sweep the living room. You just swept the dust under the rug. Well, aren't you cute.