Scrivener’s Options window and options (File>Options) have been streamlined. All of the old options are still there, but have been reorganized, and a few new things have been added. If you haven’t spent much time in the Options window, definitely check it out. You might be surprised at the behaviors and appearances you can change to meet your preferences.
For example, if you've ever been confused when you closed a Scrivener project with intent to open another, and found that Scrivener had also closed, I recommend turning on “Show template chooser when there are no projects open” under General>Startup. This allows you to close all projects, but keep Scrivener open.
NOTE: If you want to copy over your preferences settings from Scrivener 1, see Transferring Your Preferences to Scrivener 3.