Main difference is permissions, cleaner UI for normal users, and account keys use permissions assigned to servers and subusers while application keys use R/W ACLs stored in the key table.
Previously, a single key was used to access the API, this has not changed in terms of what the user sees. However, API keys now use an identifier and token internally. The identifier is the first 16 characters of the key, and the token is the remaining 32. The token is stored encrypted at rest in the database and the identifier is used by the API middleware to grab that record and make a timing attack safe comparison.
Dane Everitt