IntelliJ 11 has a much better GUI for Flex (Mobile) build settings than previous versions, but there is one issue and one opportunity for improvement.
1. Defaults to insufficiently editable auto-generated application descriptor (Project Structure > Modules > [Your Flex Module] > iOS).
Building, debugging and submitting iOS apps using IntelliJ is now confirmed to work fine. Literally follow the codesigning explanation from [http://www.adobe.com/devnet/air/articles/packaging-air-apps-ios.html]. One difference with Flash Builder though is where the explanation talks about changing the app descriptor XML file, in which you have to put a few things that ensure debugging or submitting the app will work. IntelliJ defaults to a generated app descriptor, which is placed in the output path (i.e. not editable). There is no GUI, unlike in Flash Builder, to edit elements of this generated app descriptor. As a result, stuff like the Bundle ID and app icons may be (in fact, usually are) not correctly set in the app descriptor. You may then have surprise failures to debug on an iOS device or upload to the App Store. The only solution is to make a custom descriptor and edit it manually. In other words, a very incomplete and confusing implementation.
Either change 'Generated' to an option that generates an application descriptor ONCE and places it with the sources, so it can be edited, or provide a GUI to specify the elements of the generated descriptor.
2. A typical app requires multiple signing options.
For iOS, developers can have up to three different profiles (signing options) per app, for (1) development and debugging on a device, (2) ad-hoc distribution, and (3) App Store submission. A profile (signing option) is a combination of a key file and a provisioning file, for instance steven_developer_id.p12 and app_on_ipad_steven.mobileprovision. Whenever a developer switches build targets (i.e. going from debugging on iPad to debugging on iPhone or uploading to App Store), s/he has to browse for the two corresponding profile files in the iOS tab and then build the appilcation. This is cumbersome. Moreover, previously, profile information was provided in the Package AIR Application dialog. Now it is located under Project Structure (same window as under 1.). This makes the process even more cumbersome; making a mistake means lots of navigation in IntelliJ. Probably the same goes for Android, but I have no experience with it.
My improvement is as follows. First, in the iOS tab, allow me to specify multiple profiles (p12 and mobileprovision file for iOS). By the way, why provide options as to which keystore format to use if AIR on iOS uses p12? Second, in the Package... dialog, provide a combo box allowing me to choose the profile I want, as well as a button that brings me to the iOS tab where I can edit them. Alternatively, and I may be in favor of this, move the whole profile and bundled files stuff back to the Package... dialog, and include the idea of a combo box there.