I posted in the Steam forums that there is a noticeable omission/bug in Aquaria:
I've been playing Aquaria with controllers, but I noticed one bug/omission: moving the map with controller support. This is a bit annoying that I have to use the mouse/keyboard to move the map when I'm using the controller and am a ways away from either. Any plans to fix this?
Somebody has already posted that the fix is done in Aquaria's code:
The original developers have moved on to other projects and will probably not continue updating this game. Fortunately, Aquaria has been open-source for some time now, and I believe this issue (and many more) have been addressed by the community.
Unfortunately, I don't know about anyone distributing ready-to-use binaries, so you'll probably have to compile the code yourself. This isn't really as hard as it might sound, but you will need to download a compiler (Visual Studio C++ Express should work) and a tool called CMake to generate the project files. The official source code repository can be found at http://hg.icculus.org/icculus/aquaria/. Playing a version of Aquaria compiled from that version will probably disable Steam-achievements as well.
Other than getting your hands dirty with that, I'm afraid there isn't really a solution for your problem.
However, these changes have not been pushed to the Steam version. Any plans on fixing this?