Before I begin - let me start by saying - the more I like a game, the more critical I tend to be of it. With that in mind...
* I found it difficult to differentiate some of the things that I could stand on vs. some of the things that were background. For example - there was a black tree in the background which is slightly confusing. May I suggest only allowing the things you can climb on being black - it would make it easier to "read" the level without affecting the art style.
* The jump was my biggest problem. When trying to get the crate from the broken rope bridge, every time I tried to run and jump over the gap - I didn't jump. It seemed as though I had to jump before I started moving - and that felt off to me.
* There are a few little physics issues but I think you already know about all of these - the one I liked was: I climbed on top of the crate, held down E, started moving and the crate and I started moving together :)
Despite these niggles - I have to say, this is a fantastic game. It reminds me of "Limbo" and "Inside" but with the "switching universe" mechanic that always lends itself well to puzzles.
Fantastic work!