The Suits are unlocked after the Parting Gift mission.
Skill points are given right after the Skill Point tutorial.
Gravity Well Gadget is available from the start of the game.
If you are past any of these points and still do not see your bonuses try restarting the app if that does not resolve it reboot the console, If that still does not resolve it restore licenses. https://manuals.playstation.net/document/gb/ps4/settings/license.html
