After project «Invalidate Caches / Restart…» or changing «Project Structure» the Tool Window (aka sidebar with Project) disappears. It's very annoying while you have to restore the sidebar each time you add/remove/change the external libraries, even if it's just one key shortcut like «Alt + 1» to un-hide the sidebar it's still poor UX. In Visual Studio such sidebars don't disappear unless you explicitly order to hide the specific sidebar.
BTW, all subject of tool windows/sidebars management is much more user friendly in Visual Studio rather in IDEA — you can drag & drop windows, pin them to the corner/side, easily (with dragging, nit guessing with combination of pinned, docking, split options) merge and split them. Just compare the UX of tool windows management in VS 2015 and IDEA and you'll feel the difference.
In addition, IDEA doesn't remember project's perspective after project closing and the following reopening / IDEA restarting.
Let say I want to display the customized Tool Window (e.g. Mongo Explorer) along with the Project tree, I eneble it.
Now I restart the IDEA and Mongo Explorer tool window disappears. IDEA doesn't remember which tool window has been used.
In my project I actively use MongoDB plugin and display its window/panel in projects's tree.
I paid attention that IDEA doesn't remember project's perspective after project closing and the following reopening.
In other words, if MongoDB plugin's panel is displayed, so when I close the project and reopen it after that, MongoDB plugin's panel will not be displayed.