If you only uncheck displays have separate spaces, when it fullscreens via the green button on a window, it turns the other display black, which is stupid. Instead you have to do that AND redefine the green button behavior to just maximize:
- System Preferences -> Mission Control -> Uncheck "Displays have separate spaces".
- Install BetterTouchTool. During install, don't agree to window snapping and ensure you give it rights to manage.
- Select "Other" category at the top of the window.
- Make sure that "Global" is selected at the left side.
- Click "Configure New Trigger" button in the bottom part of the window.
- Under Trigger, select "Leftclick Green Window Button".
- Under Predefined Action, select "Maximize Window".
- In Basic Settings, check Launch BetterTouchTool on startup.
As a related tip, to make a window smaller but not minimize, double-click on the menu bar.