Do you as his friend agree that he is ugly? Have you tried to build his confidence. Sometimes, people will make negative remarks about themselves with hope of assurance. If it isnt given it makes them think they were right all along.
I also don't think anyone should blatantly say that he shouldnt be depressed. It's natural to feel sensitive about something we dislike about physical appearence, but especially so, when it concerns the face.
The Prophet (saw) said, that even animals have pride in their looks and forbid the cutting tails and manes of horses, of branding animals at any soft spot (mainly face) and of keeping horses saddled unnecessarily. (Muslim, Sahih Muslim)
I don't exactly know what you mean by uneven eyes, but if you mean one eye is smaller than the other then there could be a physical cause for it, i.e. an old injury (one of many causes). So your friend should see his optician first. Likewise, if the nose is crooked due to being broken, that could be fixed. Although, I dont see that as a deformity and neither should he. Cut lip? Honestly, I don't think that looks ugly. If he is sure there are no physical causes then it could be that the small imperfections are just magnified in his mind - a condition known as body dysmorphic disorder.
I feel you can help your friend by either reassuring him and helping him to build confidence in himself if you know that he is not ugly like he thinks. Or, you can point out what I did and let him decide which applies to him and take it from there.
Also, please tell the brother that women go for status, intelligence and security rather than something that will fade in time anyway. So, if his worry stems from thinking that no one will want to marry him, he could throw that thought right out the window this very minute. Most women prefer rugged looks anyway.
I'd like to end my post by saying that lots of people aren't happy about something or another about themselves. But if it's any consolation, we will be beautiful in Jannah inshaAllah. The hard part is getting there. : )