The stories of both games are heavily based on STEM, which has to be understood to get why the first game is structured the way it is. I felt the flashbacks where you see Ruvik talking to Dr Jimenez, and in some instances STEM agents as well, made it pretty clear what was going on. Also the flashback with Ruvik and his sister Laura in the barn. It's done out of sync obviously to build suspense, so you see the horror of what they are, then the flashbacks show what made them into such monsters, and puts it all in perspective.
There are no invincible then killable enemies though. Only Ruvik himself is invincible. Those other appearances are his Dopplers he cooks up to terrorize and trap you into thinking there's no escaping his world. This is made all the more evident in the place where all other enemies disappear once you kill the Doppler Ruviks.
QTE is something Mikami made popular with RE4, and I don't like it either, but I don't get why you say the final boss fight had too much of it. You're basically running a certain route to avoid it's swats, then shooting it with a turret, then finishing it off with a RPG and a timed pistol shot. Where do you get QTE in all that?
As Zed said, it comes down to what you're looking for in a game. To me, how much challenge a game offers has always been a high priority, and if it can do that with lots of replay value by scaling that challenge well to the hardest mode, all the better. Most games don't bother making enemies quicker and more aware on the hardest mode, TEW did. The wall mines were also better off used to blow enemies up than disarm for scrap, as they had very small disarm windows and the needle moved vey fast.
Just the standard zombie AI in TEW was far more sophisticated than in TEW 2. They could hear where you ran to, and search there, even if you were out of sight by the time they got there, they'd find you hiding in a locker. This meant you had to run until out of sight, then walk to where you wanted to hide. The zombies in TEW 2 stop as soon as you're out of sight, then just return to where they were. And the zombies in TEW were also less predictable, you didn't always know if they were dead after going down. This meant when throwing a match you had to approach them from the head if face up, and from the feet if face down, otherwise they could swat you, which is an instant kill on Akumu. They also had an easy cover takedown skill in TEW 2, which I think is a strange thing to put in a survival horror game.
As far as Alien Isolation, I've always been a HUGE fan of the Alien movie franchise, and was waiting as many were for a game to do it justice, but I felt Isolation fell short of that due to the monster AI being too simply scripted, which made it easy to figure out and evade. So for me, Isolation after the first play through became more of a challenge to evade (and especially kill if you were up to it), the Working Joes. That to me made it feel very much like something other than what we saw in that first epic movie, where the Alien itself was the thing that made you freeze in terror.