I'm at US Customs so we have pretty much the entire atlassian suite self hosted: stash, jira, fisheye, confluence and crucible, some plugins... some of the parent/sibling comments have spelled out the poor integration between stash and the rest of the suite.

Here's some additional things off the top of my head...

- search! maybe our fisheye isnt indexing all our repos properly (we just recently migrated 10+ years of svn codebases too, in addition to a slew of new git repos) but I would have hoped to be able to do deep code searches within stash itself, across many/all repos.

- project areas: Only one level hierarchy. we'd rather be able to form adhoc groups (think github organizations) under those project areas

cant think of any more right now but it's late saturday evening :) but you can certainly have your folks contact us at CBP and we'd be happy to give deeper feedback if you want it