Today the main new feature in the structure modules is the release of a Java port of the Combinatorial Extension (CE) algorithm. This contains both a version of the algorithm that can be run from command line, as well as a GUI to view the results and trigger custom alignments. Essentially this is what is available from the RCSB website from: http://www.rcsb.org/pdb/workbench/workbench.do
About the generic design for Model View Control for 3D viewers, an unsolved problem is currently how to deal with selections. Selecting ranges, chains or atoms in proteins is done using a scripting interface at PyMol or Jmol. Shall we have a scripting interface (based on the syntax of one of these) or shall we have multiple select methods that accept various arguments? Jules Jacobsen wrapped the Jmol-Biojava interface using the new interface definitions for the MVC.