This is a bit of a confusingly designed game. Not that the game mechanics felt underexplained or that the world felt too easy to get lost in (that part honestly felt a bit too straightforward), but the implementation of movement, combat and level design into the premise of it all felt so puzzling.
We are informed that the main character is a pacifist who doesn't kill. How do we implement that into the game? Give her infinite ammo and no repercussions for killing. We are informed that the main character is a spy. How do we implement that into the game? Make stealth the most ineffective way of playing. With how slow and weak the enemies are running past them is barely an inconvenience. Besides there is not a SINGLE power-up that improves stealth. As a matter of fact the Phase power-up is the opposite of stealth, allowing you to trip every alarm and just ignore the consequences.
Here's my feedback: make the enemies invincible, with your attacks only stunning them. Alternatively make the enemies explode on death to discourage killing. Make the Phase power-up give you invisibility, not invincibility. Invincibility completely trivializes the late game.