Actually, rippling effects on the background can be done very cheaply with GPU effects. If there is one thing a graphics card can do incredibly fast, it's move pixels around (on the order of billions of pixels per second even on older GeForce cards).
A particle system could be used to create squares of random sizes which displace the background by a few pixels The direction that those particles flow determines the direction of your water current.
Games have been doing heat rippling off hot pavement or off a fire source for years now and I believe it is done in the GPU.
I am not even saying MA3 should have this feature, only that it is certainly possible without a huge "CPU tax" by bitblitting sections of the background in random directions by 1-2 pixels or a fraction of a pixel and then blurring the result.
Probably a low priority thing though...
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