Adobe recommends using Citrix receiver when using Acrobat and viewing PDFs on mobile devices like iPad.
Is Citrix Receiver a free service, and exactly what does it do? Does it allow iPad users to view Flash content?
The Citrix Receiver apps for iOS and Android are free, and put a remote desktop on your device so you're able to work with the full-fat desktop versions of Acrobat and Adobe Reader. The Acrobat XI Family includes touch modes to make the experience easier, and if the software on the Cirtix server has the Acrobat Flash plugin installed then yes, you can see SWF and Rich Media PDF content on your device. Bear in mind that the files you're working with are being opened on the server - you're in effect doing a screenshare session with a Windows virtual machine.
The XenDesktop and XenApp servers required to host the apps are far from being free, so this is only a realistic option for enterprises who already use Citrix. It also requires your device has a constant high-speed data connection, so if you're trying to use Acrobat XI and working with rich media it will probably need to be on Wi-Fi.