Things I am having trouble getting used to are the opposite scrolling gesture,
It takes a few hours of use to get used to it. It's only been a day and for the most part, I've gotten the hang of it.
One thing I noticed that I don't care for is when I open up Apps and close them out they are obviously still open just like all previous versions of OSX, however, if I logout or restart computer it likes to open all those Apps up into windows on my screen. I hate that. If I close an App it means I am done with it. I know I can do the command-Q thing but that's annoying when all I want to do is to do it easily from the mouse/pad. I never understood Apple's insistence that once an App is opened it does not close
Wow! Not sure where to start...
Windows open and close. Applications launch and quit.
By clicking on the red button in the title bar of a window, you are not quitting the application, you're closing the window. It is up to the application to define the behavior of that action not the OS. Some applications quit themselves after all windows are closed, some present the user with what to do next, and some just remain open and let the user do whatever they want.
By using the red button only, you're leaving yourself at the mercy of the application, not the OS. If you want to Quit the application, choose Quit from the applications menu - you can still do this from the mouse or trackpad.
All the applications are relaunching themselves when you reboot, because you're not quitting them and you have the resume feature on. You can turn it off in the General system preferences.
To me the red X button is no different than a minimize button. And the green + button always has been useless.
The red button is for dismissing or closing a window.
The yellow button is for minimizing or hiding a window.
The green button is usually for zooming a window's frame to display as much content as possible. It does not mean maximize.
Because you believe it to mean one thing or another, doesn't make it so. They are what they are, and if you try to think of them and use them any other way, you're not going to get the results you expect.