[lapcat]

System Preferences has an "Organize Alphabetically" option. System Settings does not.

System Preferences can hide individual preference panes from the list. System Settings can't.

System Preferences search field is focused on launch. System Settings is not.

System Preferences is fully keyboard navigable. System Settings is not.

System Preferences uses tabs where System Settings in many cases uses a modal window hidden behind a button.

The list goes on and on...