As others have stated, some things are very unclear. Rather than harp and reiterate those, I'd like to offer a couple of possible "fixes"
Firstly, it would likely be more clear what "score" is if you chose a different word. 'Energy', 'Progress', even just 'Points' might've been better. Basically, just make it clear that it means more than what traditional "score" does in arcade-style games.
Secondly, the score should probably shake or turn red when it's draining, like when you take damage or when you're slowing down time. Small visual cues like that go a long way.
And, actually, the more I think about it, it should probably be a meter and not a number anyway. Have a bar that fills up as you destroy enemies, and it drains when you use abilities or take 'damage.' I think that makes a lot more sense. When the bar fills up all the way, you progress to the next stage.
Also, I kind of wish the enemies had a slightly better visual cue that they're being damaged. Maybe a color change, or flashing or something.
Other than that, a few bugs I noticed: In the last level I got placed into solid blocks and couldn't move. Not sure if that's intentional. Also, the text in the bottom right was cut off on the bottom, so I couldn't read the whole thing, which is somewhat disappointing.
Ok, enough with that stuff, onto the rest! As others have said, the music was pretty good. I like the subtle changes in the level music as you progress--I would've liked to see more of that. The ending piano piece was good as well, sat and listened to the whole thing. I'm not sure if this was intentional as an effect or not, but the music sounded like it had that crappy flash audio compression of yester-year. While it brought back fond nostalgia of playing flash games on newgrounds back in the day, the music actually sounds cool and I'd like to hear it in hi-fidelity. To each their own, of course.
I like that there's no real death in this game, or not from failing to play correctly anyway. The only death is the inevitable doom you face as an android heading head-first into destruction. I like the self-exploring/identity themes being explored here. You should try to do more with that in the story telling. Other than the criticisms above, I dig the score system. You have to micro-manage a resource that you're trying to use to progress to the next stage, but you also use that same resource to protect your character. It becomes a battle of multi-tasking: killing enemies, keeping track of your character, managing your resource.
Overall, solid entry. I think some more pre-release user testing by people who hadn't played the game before would've helped you guys realize some of these things. One can never stress the importance enough of getting people not directly involved in the game to test early and often :) Of course, such things are not always easy to do in the time constraints of Ludum Dare. Nonetheless, well done guys.