I have always been bothered by aspects of Isolation's gameplay design and story. For one I think there is a lack of interactivity in the environment that hurts some of the immersion. You look at a horror game like Amnesia or Soma, you can pick up individual items and observe every inch of them. You can manipulate the physics of the environment to complete tasks or deter the monster. With Isolation everything feels pinned down, and the game limits what you can perform. You can't pick up any weapons except in scripted locations, and you cannot jump over objects. As a result the game also feels clunky and slow.
The design of the vents also stuck out on repeated play throughs. They often felt like random connecting hallways between rooms that didn't exist for a practical reason, instead of their own vast network that could have acted like another sub level to the map.
I thought the creature itself was excellent, and I only ever became aware of the rubber-banding occasionally, although the loud footsteps did remove some of the stealthy mystique of the original monster. However, there are mods out there that fix both of these issues, so it's not a huge negative.
The story was the weakest aspect of the game for me, although it had an intriguing setup with finding the Nostromo black box and investigating its disappearance. However, I think the plot would have been more novel if the initial infestation was a result of the original "Big Chap" Alien from the first film making its way on board Sevastopol, and not just the result of people going down again to the Derelict. And if Amanda hadn't been related to Ripley at all.