Isa's also the sort who just tolerates certain people more than others, honestly. He's just prickly, and spent years with no/stunted emotions and his only friendship falling apart before his eyes, he's not actually as callously evil at KH2 initially made him seem.

And he wants to make up for his actions as Saix, you know?

(And I only vaguely know Kuja's deal from Dissidia, I've never played FF9)