Our current use case is as follows: Only experienced customers of our organisation have been informed with the email address to create requests submitting email. Other customers must go to portal to submit their tickets. Once ticket is created we want portal to be the unique controller for the ticket, all users can must go there and check ticket history, all comments, attachments,... and then make new comments or transitions. We don't want customers to add comments replying to notifications.

We encourage in notifications template not to reply to emails... but despite this, some users are still replying to notifications, tipically not experienced users and tipically once the ticket is closed, when we don't allow no more comments or attachments. So we are having a lot of new tickets with summary "RE: PRJ-XXXX: summary" and description like "Hi buddies! Thanks for your help! I owe you a couple of beers!".

So, the customization we need would be something like "reply to agent email address instead of 'request email address'".

Being able to customize the email processor would be greatly beneficial to exclude suffix's of emails from adding comments. 
Use Case: A customer emails a support email. An issue is created in service desk. Someone on the shared support email (internal to my company) replies to that email and says Hey Team, what is going on with this? Even if they removed the customer from their reply - that then gets added as a public comment and the customer is alerted from Jira that they received an update. 
This is a huge issue for startups who may have CEOs and such replying to support emails to get their team to take a look at an issue, yet should not be directly interfacing with customers.

Hello Team.

Our current use case is as follows: We want users to go to the portal to read the Knowledge Base before submitting a ticket (which means we don't want to enable the option to create tickets automatically via email), but we want the users to be able to reply to notification emails and automatically become comments.

It seems that currently there is no way to do that configuration and it seems strange. I really think it should be added to Service Desk soon.

Thanks.

The problem with allowing emailed requests is that it doesn't enforce field requirements or give users prompts on how to fill out the form correctly, nor can it give them KB suggestions. Yet, we still want to allow updating tickets via emailed comments. That's why we want this ability.

We also would like to only allow comments via email, not new requests. In addition to that, we need more mandatory fields than are currently allowed in service-desk's email handler. It would also be nice to have the other options from Jira's mail handler, like being able to add a split-regex.

We face the same situation in our environment.  We want users to go to our Service Desk portal to raise issues rather than using email.  First, it helps separate issues by type and directs each issue to the appropriate group, saving somebody else from having to look at each issue and reassign it.  Secondly, we post our top issues on the portal page making it easy to get self help for common issues.  We also provide an easy to use query field to search for help in our knowledge base.  A user creating an issue  becomes a watcher and then receives issue updates via email.  It would be very convenient for the users to be able to reply via email rather than having to go to the issue to enter a comment.  But if we enable that, users will tend to default to using that as a primary means of raising new issues rather than going through the Service Desk portal.

The knowledgebase search integration in Service Desk is one of the major reasons why my company wants to start using Service Desk instead of a classic Jira project. The ideas of 'self-service' and 'avoid tickets from being created' by letting customers find the answer when they start creating an issue, are great.
However, if customers can create issues by mail, they skip the knowledgebase search. A fair compromise for those customers who think that a login to the portal is too much work compared to sending a mail, would be to force customers to create the issue in the portal and let them reply-by-mail afterwards.

So an extra requirement would be to have a configurable message text. This text should be used in an automatic reply by ServiceDisk when a customer tries to create a new issue by mail. (example: "dear customer, please navigate to the service desk to raise a request etc...")