There are a couple of changes that were introduced specific to InDesign Server in CS6.
1) Java APIs are no longer supported. All scripting must be done using the same scripting languages as InDesign Desktop (i.e. Javascript, VB, or Applescript). It seems that the development costs for the Java APIs were too high for continued support. If you are starting development on new projects that might be migrated to CS6 or later, you probably do not want to use Java.
This does not mean to say you cannot develop your apps in Java. You can still connect from a Java app via SOAP, but no Java API calls can be made. The documentation that will be shipped with ID Server CS6 has some guidlines for porting code to Javascript, and if you need any help, just pop on over to the Scripting forum... 
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.
HTH,
Harbs