> but it's not functionally different than having an API and a system for registering API keys

No, it's completely different. The entire point of keys is avoid having to store credentials, it has nothing to do with permissioning. In the case of Mint etc., they have to store credentials because there is no token/key system being provided from the banks (ie: oAuth). In the case of something like oAuth creds are never sent to the 3rd party.

And the ironic part of this is if they banks simply provided something like oAuth then they would have MUCH more control over who they worked with and have an easier time managing 3rd party data.