Eye Sludge

In particular, Pantalone seems fixated on reminding Omega of Dottore's humanity--he insists that Omega is Zandik, the person, not just a Segment, and repeatedly refuses to accept that Omega is incapable of human feeling.

Putting aside the potentially very dark reason here (claiming that Omega is Zandik could simply be a way of avoiding the grief of losing the original Zandik--if he's still there, Pantalone doesn't have to mourn him), I think this is actually an incredible degree of kindness to Dottore.

It is clear, and not even particularly subtle, that the Segments (especially Omega) struggled with issues of self-identity, of not knowing whether to think of themselves as "Zandik" or as separate entities, unable to move on from the mindsets they were locked into upon their creation, unable to differentiate into their own people over time, unable to surpass the creator to become "real." Omega makes it particularly clear that he disdained this lifestyle and the other Segments, refusing to see them as anything but extensions of "himself," rather than their own individuals (because his egoism is a poorly projected mask he uses to hide his own struggle to see himself as an individual and not "the one who should be Zandik but isn't"). Omega ultimately craves to subsume the other Segments, becoming "the only Dottore" so that he can finally achieve a whole identity and personhood for himself. There's so, so, so much existential horror in this concept that it's hard to even conceive of how miserable a life it would be--mentally understanding yourself as someone while knowing that you are actually a something instead.

Out of everyone in the game, the only character we see actually affirming Omega's identity, telling him that he is a person, he has a name, he is entitled to the very identity he was born with... is Pantalone. Whatever his reasons--selfish or twisted as they may be--Pantalone is the only person treating Omega like a real human being, and the only one we see over and over trying to remind Omega that, deep down, he still has a human heart.

Even that final statement:

Is a powerful exercise in recognizing agency, allowing Omega to decide for himself what identity he wants to finally, finally lay claim to.

Pantalone doesn't just care about Dottore's intelligence or the benefits he's reaped by being Dottore's financial backer. He cares about Dottore's sense of self, his identity, his very existence.

And the game goes out of its way to make it clear that isn't just a one-off thing--Pantalone's been prodding at Dottore's mental issues for years, trying to get Dottore to work his way through some of his distorted thinking since well back in their relationship. The Anomalous Tree Marrow notes:

In this case, "selfishness" seems to refer to not only the idea of being literally self-centered (i.e. Omega wanting to value his own existence above the other Segments or even the original Zandik), but also to Omega's clear self-hatred. If all the Segments are Zandik, then viewing Zandik as weak, pathetic, or in need of replacement means seeing yourself as weak and pathetic; believing you are "better" than the others means first admitting that "you" were never perfect.

Omega's desire to kill the other Segments, to claim Zandik's identity, to elevate himself to the position of godhood, to fight with everything he has against the fate the heavens assigned "him", all ultimately stem from an inability to accept himself, a constant selfish refusal of reality, an all-consuming desire to achieve more, to learn more, to be more.

Pantalone, in fact, implies this with his metaphor about the praying criminal:

Dottore misunderstands and takes the metaphor literally, but Pantalone's point is clarified later for the viewers:

Over and over again, Pantalone tried to warn Omega that his views and behaviors towards himself were utterly self-destructive, that his self-centered fixation with being "Dottore" stems from an inherent disgust for "Zandik" [himself] and his very human limitations. Quietly, if perhaps too gently, Pantalone has been trying for years to help Omega rethink his fragmented self-identity and reconsider the value of his life as a person.

And it seems that he almost, almost made it through to Omega sometimes:

To an appropriate degree, of course.

Omega can never reflect too deeply on himself or his course of action, because doing so would force him to confront the gaping abyss that lies between the inflated, narcissistic front he projects and the significantly more fragile sense of inadequate "self" that lies below it.

It even seems that Pantalone was able to understand Dottore's mental needs much more than anyone else, being also the only character we see to deliberately, clearly, and repeatedly give Omega the validation he so blatantly fishes for, over and over:

Make all the jokes you want about Dottore giving the Traveler 16578698 chances to join forces, but the reason he did that was because--even while insisting he doesn't remotely care--he obviously desperately craves understanding, acceptance, and respect from others. There's a reason the very first thing he asked Pierro was "Are you going to reject me like everyone else?"

Pantalone knows that Omega--well, all versions of Dottore most likely--needed acceptance, admiration, and confirmation of respect from others, and he went out of his way to repeatedly reassure Omega, giving his praise and accolades wherever it was due, while literally every other character in the game--even Dottore's other Fatui allies!--have not a single positive word to say.

While everyone is busy talking about how much Dottore cared for Pantalone's physical well-being, I think it's incredible just how obviously that care was returned. Pantalone cared! He really did. Dottore tried to protect Pantalone's health despite all of Pantalone's attempts to self-sabotage, but Pantalone tried to protect Dottore's absolutely fractured mental health despite every action leading Dottore closer to total self-destruction.

The irony, of course, is that Pantalone's own mental health is clearly a disaster too, and Dottore has no regard for life that isn't Pantalone's, so this was one of the most obvious (and frankly sad) examples of "the blind leading the blind"--neither one of these characters is remotely healthy, but they still tried their best to help each other. Clearly neither one of them knows how to fix the incredibly broken people that they are, but they were trying! Even as their convictions and goals dragged them both further and further into the dark, they still saw each other's suffering and tried to alleviate it, where no one else in the entire world bothered.