Core should provide bounce handling (and queueing) for transactional email
Currently CiviCRM core does not provide bounce handling for transactional email. This can result in automated processes sending out a large volume of scheduled reminders, etc. (as well as user-triggered forms sending out subscription confirmations, etc.) with only manual bounce handling by humans.
An extension exists to provide bounce handling and other features for transactional emails: https://civicrm.org/extensions/transactional-emails
Arguably, however, this feature should be provided by core itself, so all civi instances have bounce handling for any email message they send.
Assuming we continue the architecture where it is the CiviMail component that provides bounce handling, a solution could be that enabling CiviMail overrides how transactional email is sent, adding the extra bounce processing and other features.
Ideally, transactional email could also be queued by CiviMail, so failures are not fatal and delivery attempts can be retried. Currently, if you are over-quota or your mail delivery provider temporarily suspended your account, then you have real problems when doing some critical thing that sends a transactional email message.