I really enjoyed the game. It's nicely laid out and the levels are very well designed. But themes go beyond coding or level design, making them easily the hardest part about making a game.
Don't get me wrong, the theme get's across fine to me, but it feels forced, without much behind it that would actually give it /meaning/. More dialogue between the watcher and you would be a nice start, and maybe not having all the boss killings be required, or more importantly, in /self-defense/.
But back to the substance of the game, the items and their uses in each level was nicely done, bosses were simple enough to be beaten by everyone, even if some logic is ignored in a couple (tentacle boss, the light. Why would severing the ends of the limbs kill it, and why is "The Light" and aggressive and slow group of ball-shooting bugs?). Seriously though, the one thing that I really dislike was the Watchers judgement on the Seedling being so one-sided. Why not just give him the dumb seed in the very first place, anyways? And of course, killing the giant lava monster throwing rocks at you while you're trapped with him in a room is murder...
Basically, more variability to how the story can go, be sure to maintain logic in the characters' dialogue, and keep up the gameplay design, although badder bosses and more character durability would be appreciated. Thank you for your contribution, and have a nice day.