He says it sometimes when they're in the middle of things, just to make Yuuta mad: You're such a nice boy. Yuuta has borne the indignity of being the nice boy of the family ever since they were little, and hates to be reminded of it, especially in moments like this; possibly it reminds him too much of their mother and sister. The idea amuses Shuusuke, though it's not why he uses the words.
He likes saying it because it makes Yuuta get rough. More rough, rather; whatever their relatives might have cooed at him growing up, Yuuta is not at all nice when he's having sex. He bites. He grabs. He forces. Maybe Shuusuke should feel insulted, if he didn't enjoy it so much.
(Except enjoy could never be the right word. Enjoy sounds like something easy or lukewarm. This is more painful than that, and more necessary.)
Shuusuke takes all the abuse that Yuuta gives him, arches into his harsh touch like it's a sweet caress. He makes sure never to suggest anything himself -- he doesn't want to scare Yuuta away -- but when Yuuta bites at his lips, he opens them; when Yuuta tugs his shirt, he eagerly lifts it off; when his hands inevitably pull Shuusuke downward, Shuusuke drops to his knees and sucks. He is as gentle as Yuuta is forceful. He can never tell if Yuuta appreciates it or not.
When he's finished sucking Yuuta off and Yuuta is dangerously close to treating him kindly, Shuusuke always smiles and remarks what a nice boy he is.
The words are his way of giving Yuuta permission to be as cruel as he wants. They may not seem that way to Yuuta, but Shuusuke knows his brother, and is familiar with the exact ways to get under his skin; he knows that if he provokes Yuuta with teasing words, it will make him angry, and provide him an opening to vent all that rage and resentment toward Shuusuke that he must surely feel.
(If such provocation makes things last a little longer -- and if Shuusuke finds it excites him to be abused by his own brother, who would never dare to be so rude to anyone but him -- that's something he keeps strictly to himself. He treasures the bruises and scratches Yuuta leaves on his skin, even as he tells himself that the violence is for Yuuta's own good.)
In another world, one where they weren't related by blood and Yuuta didn't hate him quite so much, maybe they could do this differently. They could explore one another's bodies slowly, with kind words and gentle hands, and Shuusuke could show Yuuta just how much he loved him in a way that made Yuuta happy too. Sometimes he thinks he sees a longing for that world in Yuuta's eyes, in the minutes after they've finished and Yuuta is staring off into space with a faintly troubled expression.
Shuusuke knows better than to wish for anything more than this. Instead he holds on possessively to what he already has: the heat that floods his body when Yuuta kisses him fiercely on the mouth, the way he aches whenever Yuuta forces his way inside him, the dig of nails against his shoulder blades, the searing warmth of Yuuta's cock pressed against his skin, and the sound of Yuuta's voice when it breaks on his name.