Jack had a definite unique personality of who he was, but learned from his environment

For a decent while in the beginning, Dean very openly wanted to kill Jack or at least wanted to banish him or otherwise talked about how dangerous his existence was and how much he hated him. Dean eventually moved past that, and even put effort into making the two of them have bonding experiences. The thing is, every positive bonding experience they had was still on the foundation of Jack knowing that in the beginning of his life, Dean wished harm upon him, and was willing to do it himself.

Anyway, Dean's character development doesn't go in a direction that allows him to accept any queerness he experiences, let alone reciprocate Cas's feelings. To understand this we need to understand a few things about Dean as a person.

He is not actively homophobic, but some of his actions and dialogue imply he experiences some level of internalized homophobia and sometimes projects it onto Sam. For example, he has a history of calling Sam gay or otherwise making comments about Sam's masculinity.

He is quite blatantly shown to have a crush on Dr. Sexy in Changing Channels. In addition to this, he gets embarrassed when Sam implies he's a fan of Dr. Sexy, MD — the majority of fans of Grey's Anatomy, which Dr. Sexy, MD parodies, are women. I bring this up because I think it's indicative that Dean sees being seen as a fan of Dr. Sexy, MD as a hit to his masculinity (and him calling it a "guilty pleasure" further solidifies this reading in my opinion). He gets embarrassed about being into Supernatural: The Musical's music in Fan Fiction too (again, musical theater has a majority female audience).

He acts a little weird when he meets gay couples (the first that I remember being Damian and Barnes from The Real Ghostbusters, the second is Siobhan and Kristen in Fan Fiction) but it comes off more like he's just not used to running into it.

In Fan Fiction, he does, eventually, seem to accept that fans of the Supernatural books ship him and Cas (I largely say this because he says "put as much sub into that text as you possibly can" while looking at the Dean and Cas actresses).

Dean's entire facade crumbles the second he stops trying to be an awesome cool alpha male. That facade is something he puts up to come off to everyone who sees him as a stereotypical straight white man (which the show makes clear he is not). A Single Man Tear from Supernatural: The Musical actually deconstructs this really well (no I'm not kidding). Actually Fan Fiction as an episode is really good at deconstructing Dean specifically. Dean even says as much himself at the end of the episode.

Put all that together and look at where he is by the end of the show, and I would say he's improved on his general acceptance and attitude toward queerness but not his acceptance of the part of himself that is, undeniably, into men. The result is that he won't allow himself to reciprocate Cas's feelings. I don't blame the writers for that either. It's just the result of that specific aspect of Dean's character not being the focus of his arc (I won't get into that because we'd be here forever).

I mean, I think another, perhapsmore accurate, read would be that this is Sam disassociating from himself and is basically a trauma response.

But I think a lot of Soulless is just... Sam. Just not the palatable version he puts effort into. (Which is also comparable to a trauma response anyway)

Whilst obviously the main thing that throws people is that Soulless has seemingly no empathy, I do not think thats entirely different to our regular Sam. Although he is better at being/acting empathetic, I do think he has quite low empathy in general. He can emphasise when it relates to him and he can put himself into their shoes (hence why he connects best with the "freaks", outsiders and younger siblings a lot) but struggles with empathising with others.

He is also quick to jump to logic, and seems to almost forget to be more empathetic and emotional at times. (Such as when the suggestion of sacrificing a virgin came up in s3 or when presented with a victim he cannot relate to- his eye rolls, sass and bluntness are usually charming to people, no?)

He puts conscious effort into weighing both sides of the arguments, but once hes caught up in an idea he doesn't think about it from any other angle until Dean points it out. Like when suggesting that they'll only have to occasionally harvest organs if they willingly become zombies together. He runs off his own emotions and seems genuinely shocked when Dean is rightfully freaked out.

Soulless Sam, particularly after Dean realises the fact, is just Sam without the effort. I mean you can see as early as s1 Sam sort or hypes himself up and forces a smile when talking to witnesses. He goes more into a character and often picks up on the other person's energy and attempts to copy it, unlike Dean who sort of sticks with the same charm every time and doesn't really change much when talking to different people. It comes more naturally for Dean.

And Sam drops that smile and attitude pretty quickly after turning away from these people. And is quick to run the conversation back and think of it logically.

This is not to say he isn't sympathetic, he just isn't as empathetic. Soulless obviously struggles with both. He does not really have the feelings for it, but he does remember it and try based on logic and context. "Safe space". He's just not as good at hiding that he doesn't really get it, whereas "regular" Sam does.

Same way that Sam has always been in tune with Deans moods and reacted appropriately to what Dean wants and expects. When soulless doesn't do that whole song and dance, it upsets and angers Dean. Even though it's really not his fault.

Why would the angels leave? Why would Michael refuse future Dean’s yes? Because Zachariah needed Dean to see what would happen if he couldn’t say yes, no matter what he tried. He needed him to see it get worse and worse. Even if it contradicted logic. This future can’t possibly happen, because without Michael, the angels are doomed. There is no possible future where Dean shouts yes at the sky and Michael doesn’t accept. Every angel wants to see Lucifer defeated. They all want god’s plan to play out just the way it “should”, and for everything to finally be over. Even Gabriel, who cut ties with heaven, wanted this. Leaving contradicts the very core of what heaven and angels are.

When I first watched the episode, and it was revealed that the angels left, in my mind, it meant they went somewhere so far away, that even heaven was devoid of angels. Akin to another universe. That was the only thing that made sense to me in the context of that world. But where could they possibly go? No matter where, Lucifer would find them. Unless heaven was entirely destroyed, along with every angel, where could they possibly be?

I also question future Lucifer’s motivations. We know all Lucifer really wanted was to face his brother, to get answers from god. By killing future Dean, he is cutting off any chance of facing Michael on equal grounds. If Michael is not coming, what is he trying to achieve in that world? Perhaps what Zachariah believes he wants — senseless destruction.