I like to think that games can be successful and meaningful in the story department when the experiences and motivations of the player character align with those of the player. In Spec Ops: The Line, the player’s experience of the game mirrors Martin Walker’s journey as he slowly comes to terms with the fact that everything he takes for granted is being called into question (as I've explained here). Far Cry 2 is a game in which the player character is prolonging a conflict so that the player can keep having fun (as Ed Smith points out here). In that regard, Alien: Isolation has a huge disadvantage and struggles to make the player feel Amanda Ripley's plight. That's not developer Creative Assembly's fault and they've managed an effective workaround.
The problem is that Alien: Isolation is working with a very established canon. Pretty much anyone starting the game is already acutely aware of what the alien is and how its life cycle works. It has become something cool to anticipate rather than something unknown to fear. The first movie was such a success because audiences in 1979 didn't know anything about the titular threat. Aliens and Alien³ built on that by keeping Ellen Ripley as a protagonist and surrounding her with people who hadn't yet encountered an alien (the Colonial Marines and the convicts of Fury 161 respectively). Their mocking disbelief making room for blind panic made her efforts to convince them satisfying to watch.
In Alien: Isolation, the only person aware of the alien is off floating through deep space in a lifeboat. As such, the game's story sees Amanda Ripley being hunted by an organism nobody around her has ever encountered before. She expresses abject terror, but that sentiment isn't mirrored by the player. When the alien first appears, Amanda is terrified, but we're going: "Awesome, there it is!" To the game's credit, the alien does become a mysterious threat again by virtue of the AI governing its behaviour. Much has been made of the fact that the alien doesn't adhere to any scripts and is an unpredictable wildcard within the game's systems. It's a more effective threat in what it does rather than what it is.
That's why Alien: Isolation really engaged me the strongest in its isolated encounters and the knowledge that they were unscripted, which meant they were only happening to me and not anyone else playing the game. At one point, I lured the alien into a group of survivors and then hid in an adjacent room. The motion tracker then showed one dot catching up to another. A roar, a muffled scream, and that was it. This reminded me of the scene where Dallas tries to trap the alien in the vents and it was a more effective homage to the film than any matching beats in the storyline. Brendan Keogh explains better than I could why that makes Alien: Isolation such a brave game.
The alien's omnipresence does mess with the game's pacing. The 1979 movie had to work around rudimentary special effects and costume design by showing the alien as little as possible, which made the moments where it did appear stand out all the more. There's a similar underlying tension in the game that the alien could appear at any moment, but that tension is diluted because it tends to appear all the time. It's like a game based on Jaws showing the shark constantly circling the boat. Alien: Isolation tries to remedy this by including a few sections later in the game where the alien doesn't appear, but that means the tension just drops out completely and lacks any long-term management. It's easier to control that in a two-hour film.