The mainy problem I see with game play is all the "wait puzzles" for now.
Yes, that's something I was in two minds about. I wanted to remove the whole time management aspect of the game from the remake. In the original. like you said, you had to type 'wait' very often. And if you missed something, you had to wait till the next day to see if you got another chance. But removing it completely would make the game very linear, and I liked the non-linear feel of the original.
So now time only moves after specific player actions, but to keep it somewhat non-linear you can be asked if you want to wait. This happens if you leave a room where you know something is scheduled. "Do you want to wait for xxx?" If you choose yes, the game jumps to that event. So in my view there's no actual waiting there. If you choose no, you can do other things first and come back later. This is the case in the conference rooms and Blue Hell bar.
But then there are also situations where you actually have to wait for something to happen. My idea was that players will easily fill up the time with clicking on things and reading the responses and not be aware of the waiting, it's only +/- 10 seconds usually. But I'm sorry apparently that slowed you down.
This is most prevalent in the Aleph 4 section, after that you should be fine for most of the game.
BTW, in the crate
Maybe I should make that shorter.