Finished the game and I have mixed feelings just like after Act I.
Interestingly though, the mixed feelings are exactly the other way around as after Act I!
While in Act I I praised the story and had an issue with the puzzle difficulty, in Act II I left disappointed with the story, while the puzzles tickled my itch for adventure just like I hoped.
I'm still reading through the threads though, and my opinion isn't fully formed yet. These are my first impressions loaded with emotions from just coming from finishing the game, so feel free to challenge them and point me in the right direction when I missed something important.
The most praise in both acts goes to the entire Double Fine team and everyone that was involved though:
The game is so incredibly pretty and well animated. This has to be attributed to Bagel's style, and also to the engineering that went into making it look like an animated cartoon rather than a game. This is definitely one of the most polished games that I have every played when it comes to these aspects.
Same for the music.
I have only good things to say about the voice acting. In particular I'm impressed by the German voices. I replayed Act I with the German voices and I was blown away by how good they turned out. Probably the best German voices I have ever heard in any (adventure) game, and that even without any big names (sorry if I should know all these people, but who cares they were awesome). I was surprised by how close to the originals many of the voices sounded, especially the German version of Marek. You could tell me that the English VA is bilingual and I would believe it.
The puzzles have been much much better in Act II compared to Act I. Thank you! Since there already exists an entire thread for good puzzles, I'll just write about those that I didn't like:
1) The hive mind puzzles. Expecting the player to assume that looking at stuff as Vella gives knowledge to Shay and vice versa just didn't work with my logic. It didn't feel consistent with the world, it was not required in Act I and then suddenly I have to look at a combination in Vella's space ship so I know how to wire the Hexpal as Shay? That came out of nowhere and felt like a way to force players to switch back and forth. But ok, the explanation is apparently that the player is some sort of shared telepathic link between the two as mentioned before in this thread, so I can accept the type of puzzle, but still, the execution of it gives the player no hint at all that this is even an option to consider. If I am supposed to switch, make a puzzle that actually affects something in the other character's world or something. It only occurred to me to switch to Vella when Shay said "I wish I was in my ship right now so I could look it up" or something to that effect, followed by me exclaiming "TIIIIIIIIIIIIIIM!!!" in front of my screen.
2) Putting a hexagonal shape into a square hole. I got trained as a baby that that does not work. Looking at the hole makes Alex say that it's a charging station for his Diamond Droids, so I guess it's fair, and I just forgot to look at that particular thing. Still putting this here because it's the only thing I needed help with.
3) There were some puzzles that I solved just because they were there, but otherwise wouldn't have had any motivation to solve them, but they turned out (of course) to be crucial to puzzles I did know about. I think that has always been that way though, and is expected of an adventure player to just solve what can be solved to see what clicks together in the end. I could swear there were some actual reverse-puzzles in this act too, but I can't think of any right now.
4) The hand holding with the shoe puzzle. It may be a nut to crack for some, but getting presented with a grid chart just because you answered the question wrong the first time feels insulting. In particular that the individual clues are already written down on the paper for you. Luckily I already knew how to get the solution at that point so it didn't affect me much, but I was still surprised that I'd get that slapped into my face that quickly, especially because the question comes unexpectedly and is pretty much impossible to answer correctly right from the get-go unless you have photographic memory or something.
Still overall, when it comes to the puzzles, they gave me just what I wanted: long moments of getting stuck, moments of ranting about how Tim can be such a dick, moments of joy when I finally figured it out, followed by moments of saying "sorry Tim, the puzzle was actually good and it was my fault for not getting it right away, and you're not really a dick".
Now for the story, I feel like the brilliant plot that was built up in Act I went down the drain in Act II in a way.
Suddenly Shay's parents are not computers and as has been already pointed out and discussed before, they just apparently locked themselves away in a room for YEARS making their own son think that they're computers? I just can't suspend my disbelief on this. There was absolutely no explanation given for this, and you couldn't even really ask for it, besides one time or something where it's just hand waved. I just wanted any plausible explanation, like a disease or anything. Any real parent would have shown some reaction to their kid saying "I don't believe that you exist and you're just machines." It would have been so easy to just walk out that door for 5 minutes to demonstrate that they're real. But they chose not to and there was absolutely no reason given for this at all and it took me totally out of the game's story every time I thought of it.
Reading this thread I found out some good explanations for parts of the plot that weren't clear enough for me and a lot of other plot holes have been discussed already, so I'm not going to repeat them. Overall the story just didn't feel as brilliant as Act I's setup promised it to be.
Anyway, bottom line I enjoyed Act II, was disappointed with where the story went, but I really enjoyed the puzzles. So, with both parts having awesome art and VA, but one lacking the puzzles and the other lacking the story, that gives like, 2/3 of a great game, and 1/3 of a good one, I guess.