Hi! Glad you're enjoying the game. I'll reply to all your woes here :).
First of all, if you haven't already, you may want to read the post mortem I've written. I might say things that are already covered in there.
In the defense of the level design the game was written in a week, while I also had regular job and a fresh toddler at home, which left no time to get tester feedback on the progression. Also most of the later levels were made at like 1-3AM or something so... haha.
I tried to make each level either require figuring out a single rule or reinforcing a previous rule or reinforcing multiple rules at once. It's impossible to have a single campaign which caters to everyone, because for some people there will never be enough redundant levels and others may figure things out correctly immediately. Which is why I tried to go for the least amount of stages without skipping any steps in-between. Essentially what I did was write down all of the rules for each element, then try to dissect them even more and finally create a stage for each one.
Obviously I failed (I agree with your criticisms), the chameleons and brackets are the most obvious examples, but I am not too hard on myself. The game was fun to make and everyone who played it and gave me feedback was positive about the experience :).
I think a better game would be where you had the output and had to create the input!
Btw, check out Alex Diener's LP of the game, very insightful to see how others approach the same puzzle.