The UI. Although the application is powerful, it can be painful to use. Location of information is not intuitive. There is a long list of things that I wish it did differently, including:
* I log in every time I enter the software, so it should serve up my projects, my teams, my information by default instead of me having to dig for it each and every time.
* Time lags. For everything.
* Reporting functionality, which is really important, is very limited and not intuitive. I pretty well need to export any information in order to make it useful to me.
* So many things can only be accessed from one section of the UI. For example, if I want to see what other projects a team resource is staffed to, I need to back ALL the way out and go into another section of the UI rather than just clicking on his/her name and getting more info.
The list could go on. There are 100 items like the ones I listed above that make this software inefficient for my purposes.