I've been poking around in the gfx folder in the Aquaria package, and it looks like the alpha channel on the pngs isn't being loaded correctly. Any pixel with an alpha value lower than 50% is not displayed at all, while any pixel with an alpha value greater than 50% is displayed but is fully opaque. I imagine this is really mucking up the blending used for the light rays (the blue blobs) and the current bubbles; this is certainly why the graphics all have jaggy edges.
Unfortunately, this seems to be one of a whole host of problems related to the X3100 drivers that shipped with Snow Leopard. This isn't a problem with Aquaria itself so much as it is a problem with Apple's drivers. The best bet seems to be to wait to see if OS 10.6.3 includes driver updates that correct this problem.