Hey! Your game is quite interesting and fresh.
I really liked the ambient music which made the game much more atmospheric. The puzzle mechanic is also unique and the combination of 2D/3D modes adds to the style of the game. The main character is also a nice touch :)
While I did understand the puzzle mechanic, I didn't have get a good intuition for how to go about solving the puzzles, and got stuck at the second level. I think having a couple first levels with short pillars on each corners for the 2d character to move on plus having checkpoints on the pillars would make it easier for the player to understand the puzzle mechanic better, and then apply it to more challenging levels.
In terms of nitpicks, I'd like a faster 2d character movement (although I understand this could break the current puzzles) and sound effects for 2d character jumping and picking/dropping the boxes.
But overall, it was a fun experience, and I think this idea has a lot of potential. Well done!