i'm beginning to think you have a flair for the vignette.
once again, great imagery... and an excellent opening.

there are a some issues with the syntax and sentence structure here and there. I'll only point out a few that i noticed:

"With each flash the shadows become clearer, silhouetted sharply against the illumination of their own creation."
maybe change silhouetted.
'with each flash the shadows became clearer, their silhouettes sharply outlined against..."

"This kind of pride isn't generally harmful, but it has caused some clear truths to become somewhat obscured to us."
could be something like
"whilst this pride isn't generally harmful, it has caused..."

"They seemed to be locked in a sort of cosmic dance, and whenever the two met an explosion of light occurred in the sky, the source of those flashes."
due to the placing of the comma it seems (upon the first reading) that the the two meet an explosion, not that an explosion is caused when they meet.
by placing a comma after met you prevent this, but it means you would have to change the first comma into a period. Which would probably sound better anyway.
The final phrase is a little out of place and doesn't fit in the sentence. I'd remove it entirely or replace it with something like "it was these explosions that caused the flashes."

"I turned myself back towards the flashing explosions in the sky above, and the longer I watched more and more were revealed"
i'm not quite sure what's wrong with this exactly, it just sounds wrong.
Maybe something like
"...the longer i watched the more were revealed." or "...the sky above and, as i continued to watch, more and more were revealed."

mostly it's just a few out of place words and a tendency to overuse commas, but these are fairly minor issues. Overall it's very good; i really like your stuff.

oh, and personally, like the big words :P

I thought you started off the story wonderfully. The image of tiny creatures floating into the water while large ships sailed above them sort of stuck in my mind. I think you followed up well with the wings humans built to fly.

"and have dug deep into the Earth's depths to power it all"

I couldn't really get into this part of the sentence phrase "power it all" didn't really seem to fit well with what you were going for. I think something like "harness its energy or a phrase similar might work better.

I enjoyed the story, the ending had a good sense of closure that made me believe the narrator truly came to a new realization.

One thing that I think was a little bit of trouble for me was the large amount of high level words in the story. If this is something that you think is necessary than that's fair. If not however I believe a few changes could be made. Two being to the words regolith and volition. I think that it might be a bit easier to use the words topsoil and will. Mostly because if a reader were not to understand the words than the flow of your beautiful imagery might be interrupted by them checking to see the words meaning.

Your imagery was great, my personal favorite being the fighting of the silhouettes above. I thought it gave a nice perspective of the fact you wanted to get across, that universes are made with each collision. I also think that it was an easy picture to form in the head of the reader and something that they would really enjoy.

All of this above was done for the Review Marathon which is a competition hosted by the Review Game forum. If you'd like to check out the Review Marathon and the Review Game there is a link to them in my profile. Good job with this piece.

Now everybody will wanna skip their flu- shot! What a wild experience. Complex scenes described briefly, skillfully; it was easy to picture the strange alien landscape and I’ve never heard such an apt description of chills and fever. Good going!

An interesting interpretation. You write very well, I'm impressed. However, you did make some minor spelling mistakes ('to' instead of 'two' and a couple others) if you give it one last read you'll spot them. Thx for the interesting read!