I think the default InfoWindows should be left as-is where the dev can set the exact content/style using a local template. however, AGS and A2E allows users to define InfoWindows in design mode and many users would expect these templates (well, the results of the template) to be used automatically. This makes their InfoWindow experience uniform over many different cleint apps (ArcMap, the AGS javascrip API, eventually ArcGIS.com, Google Earth etc)

so, a good option would be to use HTML generated at the server for the infowindow and use Ajax to fetch the html for the popup (or maybe an iframe for better css support?) The REST api supports feature based HTMLPopups:
http://atlas.resources.ca.gov/arcgis/SDK/REST/fs-htmlPopup.html

examples:
http://sampleserver3.arcgisonline.com/ArcGIS/rest/services/Hydrography/Watershed173811/FeatureServer/1/1/htmlPopup?f=html

http://sync.arc2earth.com/9280826/ArcGIS/rest/services/tfs/1920753/FeatureServer/0/1/htmlPopup?f=html

these Urls could easily be created by the framework, so all we would need is a simple option like "serverInfoWindows":true