#with his very extreme negative reactions to things like simon's death or the leadup to the inquisitor's arrival

[thanatika]

really good points, i feel like dankovsky's connection to isidor isn't talked about much... maybe because a lot of people focus on patho2, which so far seems to have discarded that element entirely? i think that the second half of his line you posted at the start is even more indicative of his strong feelings about isidor:

simon's "murder" is what has doomed daniil's research, since he was depending on being able to study simon to avoid persecution by the powers that be. i previously wrote a post discussing how violently he reacts to the news of simon's death on day 1, as he makes a ton of homicidal and even a few suicidal remarks in response to that (he tells eva on day 1 that he'll "blow his brains out" if he has to return to the capital empty-handed). the fact that he is apparently even more enraged by isidor's death probably indicates the high level of regard for the man -- after all, he didn't know simon personally, but he and isidor probably had some amount of continuous correspondence to be called his "selfless advisor".

and i don't think that meant he truly understood isidor: based on that yulia dialogue, they had disagreements over their different systems of classifying and interpreting the world. and considering daniil knows almost nothing about the town when he arrives, i would assume that their correspondence focused much more on daniil's situation than on isidor's work. (after all, isidor sent his son off to study in the outside world, so he probably saw some value in scientific goings-on and reached out to daniil. hell, he and daniil might have been corresponding more regularly than isidor and artemy, since it's implied that artemy was a bit disconnected before returning to town.)

the fact that they had this connection does add an additional layer to daniil trying so hard to convince artemy that isidor's intended urdurgh was simon (and by extent, the polyhedron). i think the game leaves it ambiguous whether daniil is actively trying to manipulate artemy to get his desired outcome, or if he actually believes everything he's saying. i think it's some combination of the two -- i think he has really convinced himself of his theory, and it isn't a completely baseless theory either, but the way he's pushing artemy to arrive at his version of the truth is ironically so similar to the way aglaya pushed him to arrive at suitable conclusions about the polyhedron, which daniil felt so manipulated and infuriated by.

but back to his apparent strong fondness for isidor, i think part of it can be taken as a general character trait of daniil's -- he also refers to aglaya as his "best friend and most reliable ally" before discovering her "deception", and says "we are best friends now" about block just a few hours after being rescued on day 8. (he also gives andrey some pretty glowing praise in his quest log after first meeting him on day 2). i think that implies a certain amount of emotional disregulation, despite his mask of being the rational and impartial scientist. then again, his strong praise for all three of these people does come after they've saved him from certain doom: isidor gives him one last hope when he's on the brink of having his laboratory shut down, aglaya tells him she's going to help him when he's expecting her to have him executed, and block literally saves his life when he's about to be beaten to death for trespassing in the abattoir. so it also just goes to show how very desperate daniil is for any allies at all, and this desperation feels like it's being exploited from all sides by the end of his route.

Isidor and Simon, Daniil and Artemy

There’s one line that Daniil says to Yulia that has been driving me absolutely batty. Yulia says:

“You can call these demons what you want… you may refer to the Hair Eater as ‘time’ if this will make you any happier. I am comfortable with a more juvenile vernacular. It is what I am used to.”

And Bachelor replies: “You are repeating something that Isidor had once told me, almost word for word…”

When did this conversation happen? We don't have many letters between Daniil and Isidor to know how well they knew each other or how often they spoke. How did they meet? Why? How close were they? It’s hard to say, but Daniil refers to Isidor as “[m]y gentle associate, my selfless advisor.” Assuming he’s not being sarcastic, this is high praise. It also makes me think that Daniil took Isidor’s words to heart- deeply. That means that this idea, that people can be using different words to talk about the same things, is one that Daniil is more comfortable with that he’s always given credit for. Bachelor might be more open to setting aside semantic/linguistic differences for the sake of finding middle ground to agree on.

In the introductory healers cutscene, Daniil says, “it seems unlikely that we will ever get along well,” and then a few moments later he amends that statement to, “no… We won’t ever get along.”

That sounds sad. He seems almost like he had hope that the other two immediately dashed to pieces. Before, it was "unlikely" that they would get along "well," not impossible that they could get along at all. Now it is simply "we won't ever get along." He seems uncertain, perhaps because it is against his hard logic to completely bar any possibilities without confirmation. And he is usually adherent to standard social etiquette/ideas about politeness. It is possible that certain ideologies can find overlap and find a means of coexistence. But unlikely. Termites and Utopians don't often share tables. 

But Isidor tried to teach him that they could, and Daniil tried to remember that.