If Clark already discovered his powers and everyone knows about them, he's the golden child of the village. Otherwise he'd be pretty average - think Sakura but less of an brilliant student than her. He'd come from a civilian, loving family living on the outskirts of the village and no-one would originally know he was the last son of the quasi-mythical village on Krypton. Then he'd discover his bloodline, maybe with the help of his teammates. He'd be a ninjutsu specialist - that's the easiest to guesss of the three.
Diana would be the leader. That's because she'd be most likely to look at things surrounding her with clarity and feel the want to straighten things out. She'd get aware of the political tensions and she'd get them and she'd care. She'd have come from a far away village as part of an exchange between the two cultures, or because as the daughter of the Kage she was sent there for... some reason. She'd be quasi universally trusted and respected, because of how wise and how accomplished she'd be. Diana would be good at tactics, the lasso would be an artifact removing genjutsu, and her things would be taijutsu and close-range ninjutsu. Chakra-control seems like a good idea for her, but the earth-shattering punches seem as much Clark's area of expertise as hers.
Bruce would be the 'doesn't play well with others, my body moved on its own to save you' one. He'd still wouldn't kill people because he saw his parents get murdered in front of him. I'm not sure whether the Waynes would have been a ninja family or not, but Bruce would drop out of the ninja business - around chuunin exam or so - in order to protect the people of the city without having to obey police/ANBU rules, and he'd play the part of Millionaire Playboy Bruce Wayne. He'd probably be good at traps, and he'd have to rely on taijutsu alone, because he wouldn't have chakra. To make up for it, he'd rely on smarts, theatrics, and dirty tricks to make up for it. And shuriken. He'd like the shuriken. Everyone out of his trusted people would think he used some genjutsu and discreet ninjutsu, though.