I know this is an old post, but I am facing the same issue when calling my .Net Web Service methods.
If I test the calls from IIS is pretty fast (average 6 seconds) for a complicated call. However, from Flex this time is doubled. I used flash.util.getTimer() method to calculate the time elapsed from when i make the web service call until I receive a response back. So, not GUI rendering is part of this measurement.
I am also using the proxy classes that Flex auto generated for me when connected to my web service.
Same issue for me also. Data parsing from service to flex object is consuming lot of time.
I am using Axis2 webserive connecting to weblogic server.
Any solution or alternatives to this issue?