You can rewrite them or skip them. So can your players.
We enjoy them, as the players find it fun thinking of ways to utilize them. They also get my players to play a bit outside of their normal box, and more like characters in an Alien movie. Ymmv
Same for us. We've played Pathfinder with unwritten rules (don't steal from the party, split treasure fairly, no PvP, and so on) for so long that the Agenda mechanic is fantastic for us. It fits with the whole focus of ALIEN being a shift from "exploration, combat, level up ... oh, and roleplay" to "roleplay ... oh, and try to survive."
I can understand the criticism for a campaign, but Agendas are for Cinematic play. And they're not as simplistic as they might appear at first glance. Sure, Cham's deal is "I'm a good guy, and these people are my found family to be protected," but what happens when (as in our playthrough of CotG) the family begins shouting at each other furiously and almost come to blows? There is a lot of latitude for Cham's player in the written Agenda.