So far on my S run mission 9 backup, back down. Has proved one of the most challenging if you don't intend to spend quite a while going through the whole mission at least a couple times and destroying the bonus vehicles which are essentially required to S rank it the normal way.
Although exchanging words with one of my buddies about this he told me about the fact that It's apparently, stupidly, stupidly easy to get the no trace bonus on this mission... That alone is enough to S rank you.
So basically the key to getting a really easy S on this mission are as follows, you need D-Horse and a fulton upgraded to recover vehicles.
Don't use any of your equipment and items for the mission, no grenades, decoys, mines, anything... Just leave D-Horse in the middle of the road.
When the first Russian armored vehicle you see pauses on the road to honk at D-Horse and get it to fuck off; just sneak up and fulton the vehicle, then back off out of the road. Use your cigar to "blow" the rest of the mission time, then get out of dodge.
If you got the no traces bonus you just S ranked one of the hardest missions to do so conventionally in the game.
For most of the other ones you can basically just perfect sneak them with no kill bonus/no reflex bonus as quick as you can for the rank. With the obvious exceptions being missions where combat is inevitable.
Mission 9 was fairly unconventional to try a S rank but with this method was actually comically easy. Plus saves a crap load of time because otherwise It's a long ass mission, especially if you have to attempt it a minimum of two times. That's like short of an hour.
Fuck that, just use a horse and a balloon. Otherwise getting an S on this is in all likelihood going to be a phantom pain in your ass.