Crucible/fisheye - slow. I mean really slow. Unusably slow both with respect to the UI and back end. Half our team use IE which it just doesn't work in at all. Chrome is the only thing it just about crawls along in. Incredibly difficult keeping it alive with 50 users. Crashes once a week entirely and sometimes refuses to start with no error messages at all.
JIRA - workflow crash took our team of 30 devs at the time out entirely for 2 days. Overcomplicated administrative mess especially with respect to plugins. Reindexing takes out the entire JIRA instance until complete. Permission schemes and workflow is an epic mess of cludges.
Both products: Null pointer exceptions galore, scary memory ceiling. Integration sucks - all the horrible mappings to maintain.
They feel like bloated, slow and badly designed products which is worrying considering the cost.
TBH their support are good but I shouldn't have to use it on a product suite that costs that much.
How are any of these reasons that HipChat is "about to be ruined"? Both of those are huge products, and afaict were developed by Atlassian - not acquired.
Atlassian has made two big acquisitions that I know of (Bitbucket, SourceTree), and in both cases the product was better off after the acquisition.
From what I see, Atlassian goes in and provides cash and infrastructure, leaving the teams that were responsible for the product's success to continue making great things. I don't see any indication that things will be different for HipChat.
I agree with crucible/fisheye being slow, but they have greatly improved it lately.
As for the UI you basically have to run a recent firefox/chrome/chromium.
All your other points I somewhat agree with but to their credit they all improve steadily each release.
Be mindful that the products were source individually from various places and need a lot of work to look and work together nicely.
Let me finish on some faint praise: they are by FAR the least worse of all the 'enterprise' software we use :-)
Get onto Atlassian and get them to help you (at least with your slowness and crash issues) - their support is good once you get them engaged.
I've had all the problems you describe (large instance - 100k issues, internet facing) - sometimes it's as simple as a resetting a bad VTL template. They will get to the bottom of it.
Unfortunately, due this responsibility being approximately 5% of my time, I don't have time to invest in to-and-fro with Atlassian. I expect something to work (ironically like Trac did - its predecessor).
On the positive side, we're upgrading to latest versions soon.
My personal experience is that JIRA is an unmitigated UX design trainwreck. Most of the UI pages and workflows that I've seen are nightmarishly kludgey. It makes Bugzilla's UI seem decent by comparison.
I haven't used their other products (other than BitBucket, which is fine, but hasn't kept up with Github), but JIRA desperately needs a UX design vision.
We are working on re-working the JIRA UX right now and we would love your feedback. Shoot me an email at james@atlassian.com and I'll pass it along :-)
(I'm not an Atlassian fan)