I think that Maura and Daniel have chemistry, and that their relationship / marriage is real. Maybe just at some time-limited point, but I believe he does exist.
Sure, she also has a connection with Eyk, but she hesitated quite a long time to tell him that she also has that letter and that she's seeing things that shouldn't be there.
Having somebody else live through the same things as her could've helped her staying sane throughout all this madness, and yet she decided to play alone as long as possible.
Her main interest seems to be herself, always, and it wouldn't surprise me if she were an antagonist in the end, too. What speaks against this is the fact that she helps Tove early on, but her scientific interest simply might be stronger.
I wonder if her connection (if you can call it that) to Elliott is because there is some part in her brain remembering things, or because it's the classic "I was told I can't have children and I suffer from it, so I adopt the first random kid I see"?
Due to being face blind, I still have no idea who's on the ship at the very end. I do believe that they are in space and that this is most likely the actual reality, not another simulation, but the reason remains a mystery to me...
Some say they needed to find a new habitable planet and used the time to work with people's minds to strengthen them, and that her brother was supposed to take care and went mad instead.
But living through this also has a high chance of breaking them, no matter whether the simulation initially was supposed to be a positive experience or not. People usually don't really do well with actually believing in things to be real, only to find out that they weren't...
Also somebody pointed out that the coordinates only have two values, while three being actually needed. But the third might be hidden somewhere throughout the series, who knows.
I think Daniel might be a scientist just like her, but that she went down a path he didn't want to follow her, so he tries his best to get the old, nice Maura back instead by playing the simulation game, and trying to have her make positive decisions.
Elliots room being in a grave and him reacting so emotionally to the "truth" makes me think that he was also real, but died at some point. Maybe he was traveling on the space ship as well, but couldn't survive everything due to being an untrained child.
In the end, Maura feels very emotionally detached to me.
She clings to Eyk because he's a mirror to her mental damages, whatever they have been caused by, and wants to be in the role of a mother because that's generally seen as a positive human quality.
But I think she might not be the person we saw throughout the show so far, and crossed the fine line of scientific research that's still acceptable.
The whole dialogue between her and Daniel about what is the actual reality is mildly concerning to me, because: both are valid in my opinion, but the type of reality around you is the defining part for society and humanity in general.
One can not exist without the other, because the "personal reality" is essential to your mental health, and the "outside reality" is essential for social interaction. We already do have people where these two collide, and we all know how good that works...
I think Maura might be some kind of antagonist in the end, and that Daniel still exists in some form somewhere and tries to save herself from the things she created.
This being said, I also think there's a lot of truth in the words of her father. With him being also part of the simulation, he caused a lot of misery for both Maura and Elliot who she's trying to save, and while horrible things happened on the ship she has never been actually emotionally or physically damaged (unlike everybody else). So why would she build a simulation where she's confronted with her father? Having him tell a lie would have proven her point that she's not crazy, but what he said was indeed proven to be true, at least in parts.
This seems to be a bit odd considered how much control she actually had over everything in the end, except from this truth being brought up. Or maybe not control, you could call it blissful ignorance what others went through. She barely interacts with most of the people suffering after all... Even if Elliot was only part of a simulation, this didn't invalidate her father's words after all.
I'm really looking forward to what the showrunners have planned further on, and I hope that they don't try to make it too complicated and thus too absurd.
I also think that everything we saw so far has happened in reality in some was, with all being realistic enough for every time episode to happen.