Hi,
One of our client has same issue so followed following steps :
Part 1 : Installation (must part) :
-Upgraded ArcGIS Server (and all component) 9.x to 10.1 by taking backup of few folders and recreating few services (reason : Architecture change from 9.x to 10.x + more functionality in REST)
-Well tuned services and ArcSDE & updated security things for map services.
Part 2 : Web application
-ESRI has almost depreciated Web ADF so switched to ESRI API's (Few users are still using 10.0 with ADF). I know its very difficult to create from scratch. After redesigned system work flow and upgraded it with latest technology the web maps becomes more attractive.
-Choose JSAPI over flex reason light and easy+ no need to install additional plugin in web browser to work with Desktop and mobile platform
-No converter/no tool available to convert Web ADF logic to Web API's
I hope this helps you..