A lot people online seem to think the other ending was the good ending. They blindly trusted the floating orb. I did both too just to see what happened.
I liked a fair amount of the puzzles but I also disliked a fair amount. Maybe I was rushing but many puzzles were slow and annoying to experiment. If it takes a few minutes to validate a puzzle solution it's pretty lame. Like the underwater area was all kinda slow even if the ideas were cool.
Also with its inventory it sometimes felt more like an adventure game than a Myst style game, which I didn't like. Made things feel too artificial and restricted. Like for example how most of your inventory disappears once you go underground, so you know everything remaining must have a use.
I enjoyed the self contained puzzles and some of the others like the "Indiana Jones sand weight" one. Gave it a 5/10 in my notes. Had a major performance issue every time it autosaved.
Wait a minute, I just realised the ending you chose as good. Nah, trusting the orb was the good ending. The guy clearly went crazy and also ruined all the ancient buildings for power. Sharing the tech would of destroyed everybody and everything... maybe what is good and what is the bad ending isn't as black and white as I thought.
I enjoyed the underwater section, I didn't spend too much time on it. I found the second half of the game easier and I'm not sure iif the puzzles got easier or I just had a better understanding of the puzzles in Quern. Kind of like when you do cryptic crosswords from different magazines/newspapers, they have their own style and takes a few solutions to get into their mindset
I didn't feel like there was much experimenting like you say either except for one occasion when I was like "nah, I ain't doing that". That was the different effects of the berries. It felt like it wanted me to find where I needed to use the berries and find out which one I should use at the same time. I confess, I used a guide for that part.
I didn't mind the the puzzles being in a linear fashion but I do agree that you should of kept the items you collected instead of just leaving only the items you need.
I also like the way you could take not but didn't really find a need to use it that much other than to take a load of notes to get the achievement lol.