I would add a top-level subject code roughly corresponding to the arXiv math.QA.  Currently my field (quantum groups, knot invariants, TQFT, monoidal categories, etc.) is listed under 16T, 17B, 20G42, 58B32, 81R50, 57R56, 81T, 57M, 56L37, and 18D.  But there's no top-level classification that's appropriate, I end up having to describe myself as 17 "Nonassociative rings and algebras" which is terribly misleading.  Math.QA is perfect, and the MSC just doesn't have anything like it.