I agree 100% with the assessment that Act 2 is just not the same as act 1, in a number of ways. Act 1 set up so much great stuff. So much potential!
Here are the bullet points of what I thought:
Shay's parents should have stayed as robots. By having his parents be real people it makes the entire ship's decor seem pointless and the parents look like complete idiots. What on earth would the parents need to be doing all day? The entire ship is self-maintained. How would they, as adults, not start to get suspicious? If adults are on-board, why make the ship look like it's built by fisher-price?
Why would the alien guy in the ship want to be there in person and not just use a simulation or something else? We're expected to believe he just has been waiting for 14 years to finally be able to move to phase 2 of the mission - and get Shay to be "heroic, brave" etc? Having the main alien be on a monitor, reveal their evil plan and then show the little old lady as one of them? c'mon.
We never got to see inside the major city! What's in there? The game should have practically started in there!
You end the game with Shay and Vella meeting again - but that should have been about an hour or so into the game - with the rest of it taking place beyond the plague dams (new screens please) and finding out what's going on and stopping it. The entire act 2 should have been done in a few hours and moved on. It's like there's a missing 3rd act of broken age.
Why were the characters able to transfer information or coordinate events so well when they never said anything to each other? It would have been so much better if they had been able to communicate together, learn something about each other, and help with puzzles. At worst it could have been a chron-o-john like device - sending small objects back and forth - better yet, if the majority of act 2 was spent inside the plague dams working together, it would have been way better.
I think this article sums up my thoughts: