I read your post on the front page where you asked for input. I'm going to give you some feedback on the post-compo version. I'm not going to rate that version obviously. This is only to give you some ideas on where to improve
First of all, I think you had a very solid idea with your game, using the two modes as ghost and rock works fairly well as a puzzle mechanic and zooming the environment was a really neat idea.
The graphics are nice, however personally I prefer true pixel sizes over mixed-pixel sizes. What I mean by that is that you should choose a game resolution (e.g.640x480) and everything on screen must fit into that resolution. You can still scale up objects by integer factors (2x, 3x), but they cannot be smaller than your game resolution allows. As an example, look at the visual effects when the stone blows out air. The pixel size of that effect is really low, and much lower than your character's pixel size, which gives it an inconsistent design.
I really liked the ghost animation. You can give it some more personality by creating a 3-frame idle animation that keeps playing whenever the ghost doesn't move.
Your camera motion is quite nice. I noticed that you precede the motions of the ghost, which is cool. However you should fix the camera wiggle you get when hitting a wall and when you change direction. Try a more inert camera that can only move a maximum distance each frame. Also when you scale, the step size is too steep. Lerp the scaling between your current and the new size, that way it will feel much smoother. The sound you play while scaling was too long, it can't be longer than the scaling actually takes and should probably be much shorter than that. Definitely so short that it doesn't sound choppy when you scale multiple times quickly.
Your terrain collision detection needs some work. When in stone form, I was able to move through certain blocks and got stuck in others.
Background music is missing, so maybe play around with some spherical music, or maybe go with some ambient sounds. [Agaric Abyss](https://ldjam.com/events/ludum-dare/38/agaric-abyss) created some nice wind sounds in bfxr for example. That could be an alternative if you don't feel confident composing. The music you do have isn't too bad but a bit too loud which can seem jarring.
When introducing your game mechanics, never ever confront the player with a wall of text. You could have achieved the same thing with under 30 words if you just clicked together an image containing your assets, some arrows and a few pieces of text. Players are not stupid and have likely played games before. The brain can pick up these image overviews very quickly, but reading a long instruction manual is really boring. I only skimmed the text and totally missed that the mouse wheel plays an important part in the game.
The thought bubbles were for the most part superfluous. Again, people are not stupid. When they see a red wall with something interesting behind it, they assume they have to get past the wall. When there's a red switch later on, they'll figure out how it works. Some of the fire monster had a thought bubble which appeared to indicate that you have to kill them and not the others. This is totally confusing. Get rid of the thought bubble and give the invincible monsters different graphics, best design a completely different monster/turret for that so the player can distinguish them from the soul-giving foes.
Personally I would have preferred to have lives in the game. That way you can make the experience more challenging without being too frustrating by getting insta-killed.
Finally I had trouble finishing the first level. I didn't figure out how to turn back into a ghost. I assume the stone form locks the scaling, so I didn't fit into narrow spaces afterwards and since I couldn't turn back into a ghost, I was stuck. The first level requires 3 souls, but I was only able to find 2 of them. Maybe this was due to the scaling, maybe they could have been more visible, maybe I was just frustrated.