Getting S-Ranks on all missions is much easier this time than it was with Peace Walker. The requirements are fairly generous allowing for players to take their time, restart checkpoints and even get kills in some missions. All S-Ranks can be earned playing on Normal.
The two main keys to getting high scores are using stealth and neutralizing enemies through non-lethal means. There are point deductions for kills and alerts, so often it will be better to restart the checkpoint than to continue after being seen or getting a kill. Rescuing hostages also provides a significant point boost and can help increase your score if you're struggling on any particular mission. Try to avoid using Reflex as that also grants a bonus.
Maka has put together some great S-Rank videos that should help get you through any mission.
Please note that S-ranking the Jamais Vu mission is not required for the trophy. Thanks to The__Noid for confirming.