The major issues we experience are:
1 - performance when opening Configuration Manager (querying the database to get a list of projects takes time).
2 - when administrators/users have access to a large number of projects, when selecting a project from Quickstart or PRO and click OK, Empower will return a message saying "Please select a project to open". The only way around this is to open it from Configuration Manager from the right pane (opening from the left pain will open a "Global Projects" window that is empty; the same window when trying to open multiple projects at once however, there is nothing in the list). This started happening as our database grew so I cannot pinpoint the what the threshold is.
I hope this helps.