Not sure what you want to work differently.
Command-tab switches between applications, whereas command-` switches between windows of the same application. It has always been like that; the only thing that complicates matters in recent versions is fullscreen, especially if you have different windows of the same application, where some are fullscreen and some not.
With fullscreen, as with multiple desktops, you can use control-right arrow and control-left arrow to switch.
Of course every user has personal preferences on how to work.
I prefer not to use fullscreen applications, and have only one desktop.
As I am writing this, the frontmost Safari window takes up most of the screen (but NOT fullscreen, still have the menu bar).
I can easily switch to Mail, or whatever application I need (usually running about ten of them).
Command-tab is my friend ;-)