I've used shockwave for a couple of years now on sewage and mold damage, and I've never had a problem passing a clearance. I've never used Microban, so I can't give you a perspective on that, but some of the benefits to shockwave-
2 oz/gal dilution ratefor most applications
Light odor, smells like a cleaning solution
EPA registration covers pretty broad spectrum
I believe Shckwave is sold for about $40 a gal, undiluted, which works out to about 64 gallons of RTU. On Jon-Don, they advertise Microban as 1,500 sqft of coverage per gallon at about $26 a gallon.
The big benefit to using Microban, as I see it, is name recognition. The Microban name has great exposure, it is on baby change tables and grocery carts, among others. These are two recognizable items that people put their delicate valuables (babies and their food) in direct contact with, and can be used as a point of discussion to help calm down consumers who are wary of chemicals.
It basically boils down to cost and use you need it for. If both are registered for the exact same uses, than it would basically come down to a cost decision. If you have a specific use that one is registered for, and the other is not, the choice has been made for you... "It is a violation of Federal law to use this product in a manner inconsistent with its labeling" is a very true statement.