Now, there is nothing wrong with new versions. It is nice to see the USGS actively working on new functionality. The only problem is that authors of new packages and processes are not consistent in terms of which version they base their new code on. Each one uses a different version of MODFLOW2000 or MODFLOW2005 and there is no process in place at the USGS to merge them all into a consistent framework. For example, there are several very interesting new codes on the USGS web page, including:
MODFLOW-VSF - variably-saturated flow - based on MODFLOW2000 V1.15.00
MODFLOW2000-FMP - farm process - based on MODFLOW2000 V1.15.03
MODFLOW-GWM - Groundwater Management (optimization) - based on MF2K V1.13.00
UZF1 Package - unsaturated zone flow - in MODFLOW2005 V1.02
SEAWAT2000 - seawater intrusion - based on MODFLOW2000 V1.15.00
Obviously there is no way to mix options from the various package and versions. And Arlen Harbaugh explained to me that it would not be an easy task to merge all of the versions. This, of course, makes it very hard for software developers and modelers to make sense of it all.