To be fair, I see Mass Effect as a masterpiece of a similar, but different kindI just think the combination of what they did is good enough to call it that.
MassEffect.atmosphere > BatmanAA.atmosphere
BatmanAA.polish > MassEffect.polish
BatmanAA.gameplay > MassEffect.gameplay (ME contained much more tedious running from A to B and back again)
MassEffect.worldDesign ~= BatmanAA.worldDesign
MassEffect.music > BatmanAA.music (ME's music is the best game music since a long time)
Overall I would judge Mass Effect to be a better game, but Batman AA is a seriously fun game to play. I would rate Batman AA also above BioShock.
One thing that bugged me in Batman was that some areas we real "game areas." There was no good reason why a construction like that would ever exist in the "real" world. And I'm not even talking about the in-door gargoyles.
Anyway.. there are no masterpieces when it comes to games. The reason for this is that too many people are involved in the creation, and there are too many factors. Mozart was just a single person who only made music. The more factors there are present in an object the lower the chance there is that something will ever be considered a masterpiece.
But Batman AA will be on my list of 100 best games ever made.