As Chance said, the controls and atmosphere are very good. The art style is is also very striking and well polished, but I some of the sprites for the characters are a little too hard to read. The sound effects work well enough, but I think if you broke away from the 8-bit style you could get more effective results. For example, the crate sound effect could be a nice, heavy, echoing boom instead of a dinky little hit. The gameplay is where things start to fall apart. There are only so many puzzles you can get out of crates, and by the time I gave up the puzzles were getting rather stale. Part of that was that the puzzles grew in size instead of in meaningful mechanics. The last puzzle I attempted was so large that I spent more time backtracking than thinking. And then when I finished backtracking I would realize that I had to backtrack again because there were too many switches to hold in memory.
I would actually really like it for you to come back to this game. A few more interesting mechanics and this could be something really special!