Both JIRA and Confluence could use upgrade script improvements.

1- Migration of web.xml and server.xml files
2- Migration of extra certs and cacerts file
3- Migration of crowd.properties file
4- Choice of backup location, not just parent directory
5- Choice of starting immediately or not at all

Migration of web.xml and server.xml files
-I would have to guess that most folks run over SSL and change the keystore password (and possibly location) and therefore the default server.xml doesn't work.
-I would also have to guess that most folks up the session timeout in the web.xml and therefore the default web.xml doesn't work.

Migration of extra certs and cacerts file
-Extra certs and an updated cacerts file seems likely for most users.

Migration of crowd.properties file
-If you utilize crowd for auth, this file has to be migrated, the default file is wrong.

Choice of backup location, not just parent directory
-It is odd to backup to the parent directories, would be much better to give the user a choice.

Choice of starting immediately or not at all
-Normally I like to check things over before starting it back up. Might be something the installer forgot (in the current state, all the above things).