Some of the issues we had with Phabricator:
1. Phabricator is actually a suite of different applications that do specific things (e.g. source code hosting, issue tracking, project management, ...). Although Phabricator ticked all our feature boxes, some of the components it ships with are very immature and/or don't get a lot of attention from the development team.
2. For some reason the platform as a whole feels like a CRUD layer on top of a data model. The UI and various workflows in the applications are very tightly coupled with the underlying data model. I guess that makes it easy to develop and maintain the various core applications of Phabricator, but it doesn't make for a very user-friendly or usable product.
3. We have ~150 internal repositories, we actively work on ~40 of them at any given time. The source code application doesn't seem intended for that many repositories (e.g. navigating to a specific repository is non-trivial)
4. Phabricator has a fundamentally different approach to "pull requests". It works really nice, but only if you commit to using the Phabricator Way Of Doing Things. However, our team has been working on Github.com for years, and we're so used to the Github-workflow that we couldn't get used to the Phabricator workflow.
In the end Phabricator just wasn't the right tool for us. It definitely has some attractive properties: it's easy to install and upgrade, the command line tools are solid and provide all functionality you need, and it performs extremely well even on a small EC2 instance.
(EDIT: formatting)