Empathy and compassion
From NT and onward, a softer side of Kuja blooms in less restrictive environments. This development soars to even greater heights in OPERA OMNIA, where he develops heartwarming friendships with Laguna and Raijin from FINAL FANTASY VIII. But Kuja's ability to recognize himself in others takes a positive turn as early on as in 012, when he comforts an uncertain Cloud and frees Terra from Kefka's mind control during the gods' neverending war.
Kuja: So, do you plan to follow that harlequin's orders till death? I wouldn't be able to stand being some idiot's pawn—without will or emotion.
Terra: . . .
Kuja: Hmph, I've changed my mind. Let's show your master my powers in another fashion. Whether you possess a will depends on you. Go forth to wherever your feet lead you. I shall break the bonds that tie you—his spell that confines you internally.
(It's a right shame that the localization never acknowledges the inherent awkwardness of Terra's name for Kuja, because she's called Tina in Japanese.)
In spite of his capacity to do good now that he's learned to focus outward, Kuja shuns the heroic persona by claiming aloof acquaintanceship and selfish caprice in the aforementioned cases. Even when both parties try to thank him, he denies any kindness on his part, choosing to distance himself instead. OPERA OMNIA elaborates on this evasive habit by pointing to his remorse for his time as Garland's angel of death. Because the weight of his sins sits heavily on his shoulders, Kuja is reclutant to admit to his better nature on top of his general awkwardness as someone who'd previously been so self-serving. This is where his likeness to Zidane makes itself more apparent: The Ultimania states that Zidane dislikes having his inner self perceived by others, preferring to avoid showing the depths of his heart if he can help it, hence his outburst at Pandemonium. Kuja's behavior throughout the DISSIDIA subseries suggests that he's the same way, albeit for different reasons; consequently, where he once deceived for the sport of it, he now lies to remain unseen by those around him.
Many of Kuja's actions in DISSIDIA are informed by Zidane's influence or the similarities in their natures, reinforcing the latter's belief that they easily could have switched roles in the story of FINAL FANTASY IX. Once the former is allowed the freedom to explore new experiences that life has to offer, his interactions with those like Laguna—and even a character in the collaboration with Another Eden!—demonstrate how much of Zidane's kindness he's internalized by going as far as to quote him when responding to another's pain with compassion.
Laguna: I guess this was all for nothing. The fruit report's probably useless too . . .
Kuja: I disagree. Nothing's useless. Everything has a purpose, even this little detour we took.
Not every good deed is committed with purpose. In the cases of Ovjang and Mneijing, Kuja asks himself why he'd help a couple of puppets reunite with their master after the fact. When he questions his own actions so, it implies that his intentions are sincere and not rehearsed with ulterior motives in mind (as much as he'd like to claim otherwise).