Failing to capture the orbital containment sphere before it falls into the atmosphere and disintegrates would mean that Daszk dies a horrible death, as he's trapped there with no way to get out...
If you don't recruit Chac, it's extremely likely that he dies in the destruction of the Inquiry, since he's suicidally depressed, and therefore wouldn't bother to evacuate...
Cassidy and Cole make a Heroic Sacrifice in the optimist ending. Logic dictates that if you don't recruit them, they still live happily on their Surface after the events of the ending. By recruiting them, you are essentially signing their death warrant. True, it's their choice, and all, but...
Why is there such negative stigma towards cyborgs? There apparently wasn't any in Cassidy's time, since she said AUGs didn't have a separate classification, and people were suppressed soon after that, so it must be a relatively recent development. Science is apparently so developed that cybernetic parts are vast improvements on organic functions, anyway, so you think people would be lining up to get augments instead of being all "OMG I AM A FREAK" when being forcibly augmented to save their lives. Really, it's a surprise they haven't invented full robot bodies yet.
Endgame spoilers here, sorry for the wall of spoiler, but: So the reason the Progenitor was attacking everything in episode 5 was to get Ros' attention. However, after he confirms that he's found Ros and they have gotten to safety, why does he then be a Jerkass and destroy the Inquiry anyway? Why does he not call off his assault on the Machinatorium, for that matter, since he now knows that Ros isn't hiding there? In sum, why does he act so cruelly when he's trying to get Ros on his side? Is he just crazy?
In a world of immortals for whom death is a concept foreign enough that they forewent reproduction, the Progenitor is the only one (as far as he knows) who is losing immortality. That is bound to throw almost anyone into a state of Sanity Slippage. So yes, he's just crazy.
If the Progenitor noticed he was aging, why did he continue to stay in one place, making the effects as pronounced as possible, instead of making the Core mobile, thereby delaying him by relativity? He even notes that this is the reason why he's the only one to feel the effects so far.
As far as I know, none of them knew if Neff would be able to hold the ground (pardon the term, I know there's no ground in space) on their own. And sometimes choices made due to not knowing if one person would be enough lead to more people sacrificing themselves when it is not necessary.
Thomas' What the Hell, Player? speech is negative regardless of what choices you made; he will always criticize you. Why? Is he just that much of a Jerkass that he can't be pleased by anything Ros does?
He is a Jerkass, yes. But he does have a point in that every choice you take can have consequences. Look at Lazarus and compare it to how Ros is. The pessimist ending even explores that further, as it makes the two quite similar.