Maybe you just don't play with flawed humans but while every group I've played with can come together to work as a hyper-competent team, I've seen the same groups break down into every man for himself routs or develop in party rivalries or see one character sacrificing party interests for the sake of his own. I find I don't really have to encourage in party conflict. It's going to happen anyway.
And Stress is a great way of simulating the flaws in people.
Oh, I play with flawed humans, I can definitely confirm that!
But how flawed their characters are really depends on the game. D&D has told everyone for decades to eliminate risk and to always take the optimal route. Flaws in 5e are, as presented, easily and very often ignored.
What's funny is that the agendas in Alien are also easily ignored. It feels a little more wrong to do that in Alien, though... which is interesting in and of itself.
I think there are a lot of things I didn't really enjoy, but I'm against the crapsack setting, And I'm against using the agendas to enforce that. And I'm against the limited focus on PC's versus what are effectively GM pets, not necessarily in this case because you have a GM emotionally invested in the monster winning (which I certainly didn't have in the one shot) but because that's true to the movies tropes. "Alien" is a case of an RPG that does one thing and does that one thing well, and I'm always against RPGs that just do one thing well. Ultimately, I'm finding I'm not that interested in playing a serious game where the PC's are the characters in a slasher flick. "Michael Myers" is not an interesting RPG to me, because even the name would imply that the PC's aren't really the protagonists of the story.
All I can say here is that this is not at all how the game played out at our table. We had five players, and two had PCs that died. The rest made it out.
I do agree that part of the game is "can we make it", but I actually think that's a good thing. I think having an RPG with a focus like that is good. Though I do think you can shift that focus a bit. Certainly that seems to be the main difference between a short cinematic game and a longer ongoing campaign.
I don't think that you'd ever really want to totally abandon the "sci-fi horror" genre entirely, but it need not be at the forefront at every possible second.
Because the entire point of a single defined agenda is that you don't explore character. Your character is defined for you and to explore you'd have to play against character.
No, not really. They give you a goal for the character. But it isn't required that you follow that goal perfectly. Many of them are presented with words like "... if possible" or "... if need be" in them. There is plenty of wiggle room. And really all it does is give you a "how far will you go for X" question... which makes for interesting play.
As for the agendas enforcing the "crapsack setting", again, not how things went at my table. In Chariot of the Gods, there are two agendas that are at more at odds with the rest of the crew than others. One of those is optional, and I won't go into details because I don't want to spoil things.
The other is fairly obvious in that there's a company agent on board. The player who had the company agent was actually playing in a way to meet the orders of his agenda while also remaining loyal to the crew. The conflict for him came from the agenda and the idea he had for the character. It was actually an interesting dynamic to watch, knowing his agenda, but seeing him try not to put everyone in danger. And instinctively, the other players assumed he was working against them, so that created some interesting tension.
All of the players brought something to the character they played. I don't think your assessment of agendas as being this all-encompassing thing is accurate.