For me this is kind of a simple question...
Throughout Kotor, you get Carth questioning your loyalty and how he doesn't trust you at all. While personally it is fun grilling him and making fun of him, his character is just not that well defined. It's kind of hard to trust a guy who doesn't trust you.
On the other hand, you have Atton whom you don't know anything about at first, is pretty handy in sticky situations and is really great at certain moments. Especially when you find out about his past, that's where his character takes off.
So IMO, Atton is better