Honestly, living in that world... No, Creative Assembly knocked it out of the park.
I can't agree with the notion that "it being Amanda" somehow makes it bad. If it had been done poorly, then yes, but it wasn't Amanda's involvement not only in the story is justified from the character side of things, but also from a story side. It's logical, it's justified, and for me, wanting to know what happened to her mother was more than enough motivation for the character. The Alien films have always had a subtext of maternity.
My gripes though relate to Stompy. They nailed Stompy almost perfectly. Almost. I hate the extra jointed legs, and wish it had been a perfect 1:1 translation of the Giger design. I also wish they had gone into the Fox archives and dug out the vocals done for Alien for the creature sounds. The two shrieks, the cries of pain when it's getting hit with the gas, the drooling, hissing, gurgling noises it makes when its killing Brett and laying in the shuttle. You take all of that and you'd have plenty to work with and expand on. Plus the game already relies heavily on very subtle sweetner sound effects for everything else, including as someone else said, the Alien's tail. You change those two things and you'd have an almost 100% puritan experience with Alien Isolation.
As it stands though, the game is great. It tells a simple story and it does it very well. Does it get a little long in the tooth sometimes? Yes. But i'll take more of something good, than less.