I think it would be really nice if it were possible to create Application Assignment Profiles. This would be a mechanism where Application Templates would automatically be assigned to nodes (likely as part of the re-discovery process) that meet your pre-defined criteria which could also include a component that tells it how to decide which Credential to use.
These profiles or pre-defined criteria would look a lot like the Advanced Alert Trigger conditions; at least that is how it goes in my head.
Would love to hear if others have interest in this or improvements upon the idea!