Both fisheye and crucible are standalone applications which happen to use jetty.

I think we should change this so that a webapp can be deployed into other app servers, (like jira/conf do). This is so that other app servers can be used, and we can cluster this.

This would then lead to another really advantageous "downsides".

For instance.. instead of using hsql/hibernate, use a proper datasource, and support other external databases.
secondly, the indexies, could be made clusterable, and/or put into the database directly, so offloading searches to the DB if performance is better

finally, a proper plugin architecture should be maintained.. I know, your are slowly edging towards atlassian plugin v2. Whcih is great.