There are two reasons I can think of for moving away from USB mass storage towards MTP. One has been officially acknowledged, one has not.
The obvious, official reason, is that it should be easier to use. On my HTC Desire, I have to tell the phone to go into USB storage mode, then mount the storage from my PC, do all necessary operations, dismount it from my PC, then tell the phone it can have the storage back again. On my Galaxy Nexus, I simply run any MTP-speaking client, and am immediately able to move stuff back and forth.
The second reason, which seems a pretty obvious guess to me, is that it is to do an end-run around Microsoft’s FAT-licensing protection racket. Because the storage never needs to be directly accessed by a Windows PC, it can use any filesystem understood by the Android Linux kernel, which means it can avoid FAT and Microsoft’s patent royalties.