The first question is a problem that many people have issues with. Each successive email response adds more and more to the bottom of the message. This is more of an issue with the email server and its configuration than JIRA. Turn off the feature where it dumps the entire thread into responses to JIRA.

From the Atlassian Documentation: For each event notification, JIRA will only send the first encountered email intended for a recipient. Hence, in the case where a user is included in two or more recipient lists (e.g. the Project Lead and current reporter) for one event notification, the user will only receive the first encountered email […]

The easy answer is that Atlassian needs to protect the integrity of their system. Workflows cannot simply be imported, they are part of a bigger setup. Custom fields, screens, and issue types all come along with a workflow. It is possible to import workflows into JIRA Server, this can be done by an experienced administrator.