I can only give you my personal opinion, but it looks like you are dealing with a failure of communication on Valve’s part. This is a shame because Steam seems the perfect vehicle for Aquaria and has worked wonders for other indie games. The situation really only gives the both of you two options: move on or make some noise to get some sort of response out of Valve.
It can easily just be a post on the General Topic or Suggestion forum in the following format:
Title: Aquaria on Steam
Body:
Hi, I Alex on and released the game Aquaria (some background information), we won the following awards <list awards>, where featured in <stuff like Destroid’s Indie nation articles> and entered in the following indie competitions <Stuff like that PAX thing>.
We have talked to <list the two Valve people> but have not heard back in multiple mounts. This is a shame because Aquaria is a excellent game that features <list features, ie being a metroidvanina, 2d artwork, etc>
If any one else is interested in please visit our website and try the demo <link>
The thing is you’re already NOT on Steam, so what do you have to loose? Maybe a few of the million of people on Steam will give it a shot, maybe even more will start posting in the thread, or (best hope) the admin pass it up the chain in Valve. The sad part is no matter how good your game is if you'r not pro-active nothing will happen.