I don't think anything with Flash involved is considered "good practice" by Apple...
Kidding aside, I would go with JSON, it fits ActionScript well, since ActionScript is based on ECMAscript. That JSON has less overhead than XML can also be a good thing on a phone (less bandwidth).
Working with XML is easy in ActionScript since it has E4X, but if you should at a later stage switch to Objective-C/Cocoa, I believe JSON is betters suited than parsing XML.
What you should probably avoid is setting up a SOAP web service. In my experience, it may look as a tempting option on the .Net server side, but is cumbersome to work with on the client side, in scripting languages like ActionScript (and SOAP has a lot of overhead).
All this said with reservation for that I haven't done any development for the iPhone using Adobe's Flash CS5 packager for iPhone.