Recently went back to FT to finally finish it...long time ago, my first playthrough went bust right before opening the Vault 0, because I killed Behemoth at wrong spot and the corpse blocked nuke carrier's path.
On topic of muties...it's about finding the right tool for the situation. In St. Louis and Jefferson, you can deal with most muties simply with drive-by. Don't ever underestimate the power of your vehicles. Just don't forget a lot of tool kits and decent repairman for these missions.
In close combat, muties can be overpowered easily by two guys with Jackhammer and SAW. They usually react slowly in CBT so they can be easily ambushed by "execution squad". Set it up right, like one guy opening door to room while rest of the squad gets a clear shot on mutie just as the door opens, and most muties don't stand a chance. Most mutie encounters that aren't drive-by are this kind.
There are only two really problematic spots with muties. The "command post" in St. Louis, which doesn't have to be eliminated (but it's preferable, because you can get a lot of XP and .50 cal DU ammo), and Osceolla outside. In both situations, your biggest trouble are mutie "elites" packing M2 Browning with skill good enough to match your snipers in range and get a hit or two per spray on that distance...which is enough to turn one of your recruits into red paste. St. Louis can be dealt with, thanks to the cliff, using decent sneaky grenadier and high perception spotter. In Osceolla, your only choice is perfecting your ambush tactics. It's one of locations where sneaky trapper with mines or remotely detonated explosives can come very handy, as you can use sniper to lure out the muties into the blast zone you set up earlier.