The biggest difference between true digital 5.1 and Pro Logic II is the use of the subwoofer. It seems, with Pro Logic II, there is just not enough low end. As far as the sound goes beyond that, it is up to the programmers how the sound will work.
For example, Eternal Drakness on Gamecube has probably the best overall use of surround sound I have ever heard but Call of Duty 3 sounds amazing in a different way.
The use of surround sound is probably more important than the fact that the game has surround sound. If that makes sense.
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