There are a couple of changes that were introduced specific to InDesign Server in CS6.
2) CS6 introduces "Session Support". Calls made via SOAP can be executed in separate threads grreatly increasing performance for SOAP calls. This is different than separate instances in that all the sessions are run within the same instance of InDesign, but scripts can be executed in concurrent threads. So ID Server now has both multi-threaded and multi-instance support.