Hi,
You are correct in your assertion that there is a functionality delta between the 4.3.2 and 5.x releases. The main reason for this was that additional platforms were introduced (MicroStrategy, BusinessObjects, etc) and a standardization of the UI took place. With this effort, some features were not included. Bringing the Esri Maps for Cognos functionality back to the baseline is the major focus for the next release of Esri Maps for Cognos. These added features will also be brought forward to the newer versions of the other platforms as well.
Scott