So, what you're saying, succinctly, is that if there were a sequel, that you would like more of everything. Specifically. That is highly doable :)
Most puzzles don't have a sequential requirement and different character builds can skip some puzzles (e.g. an insane strength build character can skip the amulet puzzle). From memory I think about half of the monsters can be defeat via alternate paths.
I've always loved the idea of a rogue-lite adventure, where you could get different parts of the game/story depending on your stats/build, with some sort of procedurally generated puzzle system. Might make that one day, if I can convince my partner that spending several more years on the one game is in our best interests :D If I do, I'll be sure to give you a heads up!