Regarding the first part of the question about administrator created orders, I would agree that the current setup is robust. However there are always caveats when you start to get into the details of each site's payment setup. These situations might be a good opportunity to writing new features for existing commerce_* contrib.
For discussion sake, lets say that your users are able to save their CC info using a CIM provider. The CIM feature is exposed to the user, not necessarily the admins. At this point the admin would not have access to reuse the stored CIM on subsequent orders.
In a case like this, you could lean on more of a generic and hands on solution such as the masquerade module to allow an admin role to "switch" to that user and create the order. Not elegant, but an option for the OP.