Is there a significant change in this last major release or is this just a concise decision considering some contextual questions?
Indeed, Matt is correct. To add on to what he said, I believe the main reason is due to the significant changes made to the databases, such as schema changes and indexes. It was much more complex to upgradge via database migration, increasing the chances of something going wrong.
Some major checkpoints that show this is from JIRA 3.6 to 3.7, as well as when JIRA 4.0 was released. You can read more about this here:
http://www.atlassian.com/software/jira/docs/v3.13/upgrading.html
http://confluence.atlassian.com/display/JIRA/JIRA+4.0+Database+Schema+Changes+for+MySQL+and+Oracle
Database migration (in-place upgrade) in 4.3 became officially supported, and became the recommended way to upgrade JIRA. Previously it was considered the "alternate" method, and had not been as rigorously tested.
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As well as not having been rigorously tested previously, it also had known bugs, such as not automatically creating database indexes.
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