St Louis is the first "big" mission you get if you want to storm the fort. There is no two ways about it. That fort is nasty, ugly business.
First thing you need to realise is that there are three M2 wielding super-ultra-supermutants sitting at the main entrance. That's right, they are NOT normal supermutants. They are Psycho-drenched, ultra-armoured, HP shitpiles wielding M2s loaded with DU rounds. They are each worth over 4k XP on Tough Guy mode, IIRC. That is 10 times what a normal supermutant is worth? I don't know. But multiple times anyway, and they are commensurately nasty. A single burst of DU .50 will wipe out your squad, nevermind 3 of them. Fighting them face-to-face is asking for your whole squad to be wiped.
Second thing to realise is that there is a back entrance to the fort. It is guarded by 3 normal supermutants wielding SAWs, which is much more manageable. However, there are 2 other supermutants in the way, a grenadier and a SAW wielder. Starting a gunfight with them at close range is asking for trouble because that area is overlooked by about 4 other supermutants on the walls, all wielding SAWs. Even if you manage to use the overhang to avoid the 4 guys, you can't re-stealth as they know you are there.
So, what do you do?
Well, first thing is to clear the bloody trenches. Use stealth and ambush tactics. Clear the surrounding areas and then the trenches.
With your best sniper, use the sniper rifle to take a potshot at a supermutant at max range. Then run away. The rest of your squad should be stealthed, armed with shotguns and lying down across your line of retreat. If the supermutants chases you (most in the trenches would at least try), run right past your guys and way. Do NOT use Overwatch in TB for the rest of your squad. That is a rookie mistake as they will all fire on the first supermutant to move into range and expose themselves to the rest of the supermutant squad (if any; there usually is) on your tail, which usually results in a lot of lead or explosives coming their way. Once the supermutant squad have ALL moved into range, then manually have your guys blow them away. Remember, you can't move and overwatch at the same time. Neither can they. That gives you 5 out of 6 guys of your squad free shots at the supermutant squad before it is their turn again. That should end them before they could squeak.
Some supermutants, however, love to take cover instead of chasing. The M2 idiots in the trenches do that. In that case, you are dealing with lone cowards. A few auto-shotgun burst in the back will end them and there is no one else around to take revenge on your suddenly exposed soldiers (there are a couple of exceptions, but careful positioning would eliminate that threat). So, make them take cover and sneak up on them with soldiers armed with shotguns and close-range burst them to death before they could fire a shot.
Once the trenches are cleared, organise your guys at the eastern side of the trenches. The two supermutants on the way to the back entrance is there. Your goal is to end both of them before they duck, so sneak up to them and do called shots to the eyes at as far away as you can while still retaining a 95% hit rate. Sniper rifle and M16s both work. If you don't kill them both but did knock them out, restealth as fast as you can and come back to the exact same spots where you opened fire. Then, get out of combat and wait with Aggressive Stance on. Once they regain consciousness, they should drop dead.
Now, use your best sniper with the sniper rifle and snipe the guys along the wall. Remember that those who moved cannot fire back in retaliation, so you can run in, fire and run our again. The sniper rifle has enough power that it will do damage to supermutants even without aimed shots or crits. Keep plinking away and stay the hell out of range of the SAWs (40) and M2 (45). If they drop behind cover, move your sniper to the south side of the wall and play there. The ones on this side will eventually stand back up and vice versa when the south guys decide to play coward. WATCH OUT FOR THE M2 WIELDERS. There are a couple of them on the walls and they look the same as the SAW guys until they open fire on your ass. Their usual position is the bunker overlooking the main entrance (and they are not the three ultramutants) so you can sometimes see them runing for the eastern wall. The Awareness perk is worth its weight in gold here. You should be able to clear a large portion of the defenders that way, including some melee mutants that rush to the wall from the central bunker area. Kill those as a priority as they can fuck up the next part if you are not careful.
Now comes the twitchy bit. Sneak across the main bridge at a crawl and crawl all the way to the back entrance with all but your best sniper. Pick up the 5.56mm assault rifle along the way (the XE-whatever the hell). It is the best 5.56 weapon in the game, if a bit short-ranged for my taste (same as AK47, so it isn't that short). Have your sniper hang around the trenches on the other side of the moat. Once your guys are at the back entrance, have the sniper fire on the supermutants guarding it. They should drop down behind their fortifications. Now, crawl up the back ramp and then immediately crawl to the very north edge of the map. There is a VERY small, 1 hex corridor between the bunker containing 1 supermutant and the edge of the map. Use it. It looks like you are climbing on to the edge of the bunker, but you are still below the rim if you did it right, and he won't see you. Doubly so if he is cowering from your sniper's fire. Get all 5 guys across there one-by-one. Now, you have 5 guys on the northern edge INSIDE the fort, and all the supermutants are looking outwards.
Head for the central bunker. It has 2 supermutants in it and 2 entrances: north and west. Position two guys at the north entrance so that they can fire at only one of the supermutants inside AND they cannot be seen by any other supermutant. Do the same with the western entrance except they must target the other supermutant in the bunker and only that one. Make sure they are using weapons that will end supermutants with one blast (i.e., auto-shotguns). Flip all 4 to Aggressive Stance and fill the interior with lead. Restealth and get out of Aggressive immediately. This is where the melee mutants would usually fuck you over if they are still around as they will prevent you restealthing. Not all of your guys will be able to restealth even without the melee mutants there, but all you really need is 1 to do so (as you have that other guy in reserve who is still stealthed).
Head for the northern bunker (the one you crawled past just now on your way in) with the two stealthed guys. Remember to always be crawling within the fort until all supermutants are dead unless otherwise stated or you are dead. You should be able to crawl into the bunker behind the supermutant if he is not looking your way. If he is, just stay at a distance and wait until he turns back to the trenches. Your sniper outside would be helpful in attracting attention. Blow him away once you get into position and restealth again. The entire fort should be dead except for the 3 ultramutants sitting by the main entrance (assuming you got all of the guys on the wall and the bastard with the grenades in the tower that you can't get to; if not, the two guys should be able to kill what's left along the way) with your sniper. Crawl to the bunker next to it. It is the beginning of the wall area and you should be able to crawl from it and get to the bunker overlooking the main entrance by hugging the wall. The three guys in the central bunker should get to the south facing side and crouch under the windows. Bring your sniper to the main entrance area.
Fire on the nearest of the three ultramutants with your sniper, remembering to stay out of M2 range. Then, run away but stay within line of sight of the three ultramutants. If they make any movement at all other than rotate on the spot (i.e., crouch, kneel, get up, move, etc.), have your guys in the two bunkers pop up/out, fire a burst of whatever weapon you want at them, get out sight and restealth. If they can't restealth, bring your sniper back to attract attention. Remember, if they move, they can't retaliate fire. USE THAT. Keep repeating, but be ready to modify your tactics if they start doing funny things. Sometimes, it pays to get out of combat mode and just wait until the ultramutants lose interest and return to their original positions. Keep on your toes and you should be able to blow them away eventually without taking a shot in return.
Congrats! The fort is yours. You can loot it at your leisure. Just do NOT forget the mines at the main entrance. They are still there and you need to clear them the old fashioned way (at a distance with shotgun blasts).
Remember: WATCH YOUR STANCE. If you left your guys in Aggressive Stance while trying to sneak, you might as well restart the mission.