I would consider that wholly a positive and not a negative. Most of the time you don't want to have PC's with sharply conflicting agendas in a story you want to go on for a long time. You very much ideally want to have the party working together in a gameable story because in a gameable story you don't have the power of plot to make it all work out. Whenever you have conflicting agendas in a party regardless of the RPG, you often need OOC agreements and negotiation between players to work those agendas in a way that doesn't derail everyone's fun. Keeping agendas secret and running PvP rarely is going to work out for a longer game.
No, I think that it makes the game interesting and different from other "team-based" games like D&D. I think forgetting that pure team mentality is one of the keys to enjoying a game like this. The characters should have reasons to not get along at all times. They should struggle to work together at times.
And as I said in my last post, not every conflicting agenda needs to be in direct opposition to another.
As for the length of the game, I don't think it would be a problem there. I don't expect a campaign of Alien to be as long as a campaign in other games. Multiple sessions for sure, much more than a one shot (or the three sessions it took us to play through Chariot of the Gods), but nothing like what many consider standard D&D campaigns.
Agendas can also change over time, so that may be an interesting element.
Aside from that, the conflicting agendas common to Alien stories are part of the power of plot protection given to the aliens, as a way to derail the protagonists when they otherwise should succeed. Pulling back, they are ways for the author of the story to screw over his protagonists and make sure they never have a way out, and shocking his audience. That's fine in the medium of a horror movie. But in an RPG, the protagonists are the audience, and that's just bad GMing.
I don't share that view. I share the view more that it's the removal of the plot protection given to the PCs.
The other use in story of the conflicting agendas is a way to explain why the characters in an Alien story are frequently jumping through the stupid hoops to advance the plot. Disbelief is less suspended if it turns out that they really weren't just that dumb, they were evil and malicious.
I agree that the agendas (conflicting or not) can help drive things forward. I don't think that's "stupid". I'd argue that some group of hyper-competent people who work in total unison is far more contrived than characters who may behave in ways that are not ideal.
Your overall take on this is way too negative, and doesn't come anything close to my experience running the game... so I can't attribute it to the game nor the setting.
So the game has two play modes: Cinematic and Campaign. Cinematic mode is supposed to emulate the tension of a movie and be played in a single session. Which is laughable because you almost certainly can't play Destroyer of Worlds or Chariot of the Gods in a single session unless it's a long, long session. You use pre-generated characters and each PC is given an Agenda card at the beginning of Acts I, II, and III. For a campaign, players generate their own characters and you don't use Agenda cards (although if you're the Mother you can do whatever you want of course).
Yeah, I ran Chariot of the Gods, actually! I'm familiar with the cinematic and campaign approaches. Although I didn't recall that campaigns don't use agendas. I'd likely still keep them in there, although would have to give it some thought... as I said, having reasonable agenda for such a "mission" based scenario seems a bit challenging.