I hope projects will get rid of JIRA now!
Be careful if you use subtasks for issues, which may sound like a perfectly reasonable work breakdown idea but subtasks are snowflakes in Jira and become very hard to have visibility into, assign points to, etc
The rest of the rant I'll omit, since it's more rooted in my personal hatred for their products and has less substantiation
Apart from that, for internal company use it's been one of my favourite PM tools I've worked with. For open source with open communities, it's just too much overhead to manage.
My previous employer was a little larger (some 40 employees) and I can say that Jira solves nothing that we couldn't solve much better with text files parsed by Perl/Python/sed/awk, sometimes having a little bit of editing help (such as syntax checking on :w) from Vim/Sublime plugins (both had users that maintained their plugins).
Maybe Jira is meant for larger companies? There is a ton of special characters that trigger all sorts of crap: square brackets, double curly braces, ampersands, semicolons, colons, underscores, asterisks, at symbols, backslashes, octothorpes, pluses, carets, tildes, double question marks, pipes, and even hyphens. It takes about num_characters*20 seconds to escape a regex so it doesn't format or hide parts of it (it doesn't help that you can only check by saving, a lot of formatting does not show up in the "visual editor"), but there are probably a lot of features there that one could be using.
It's really about how the team/department uses Jira, how it's setup, and the overall process.
My last company we were ~30, and it was a total mess (although we were only ~3 developers). It's really about how it's setup.
There's a famous issue dating all the way to 2006 for this: https://jira.atlassian.com/browse/JRASERVER-9292