The unique RPG-like branching character class paths give you a pretty fantastic opportunity to categorize puzzles into "bins" appropriate for both the class type and player style.
For example, arcade sequences neatly fit the Brigand's style. Dialogue puzzles would be Rogueish, as they'd be a form of confidence artistry. Riddle/mathematics puzzles and minigames dovetail well into the sorcery of the Mage's path.
I enjoy all of the above (arcade probably the least). Inventory puzzles are a staple and should be part of all of the above. Especially satisfying (and howlingly frustrating), as mentioned by others, are the very long-running collection quests in which random shit A and random shit Z finally come together at a very late stage to combine into a grand plot advancement. Hence, I would say that a McGuffin style item puzzle is best for one of those, since reserving such a combining for practical item could be a bit punishing for a player who has forgotten to pick up a piece very early on, and loses the opportunity to do so. Nothing restoring and replaying dozens of tedious sequences, which while difficult and rewarding the first time, become a chore in successive runs. However, if you are constructing the Fine McGuffin of Power out of the mystical Three Pieces, you're unlikely to try to advance without first finding all three.
I, so far, found the structure of the inventory puzzles in the demo (that I've seen! I've not played through all paths completely yet). If that's the flavor and tenor you're going for, then by increasing the scope and magnitude of the overall finished product sevenfold, I'm certainly pleased to have put myself in the dungeon
