Stealth build really takes off around the third rank of stealth, around which time you should have a solid long ranged gun option to complement a short ranged light pistol. Until then, companions can fuck it up a lot and super mutant hounds will sniff you out from miles away. You also need to avoid wearing any metal armor prior to the third rank in stealth, if you can. Mirelurks will also basically make any stealth approach useless, outside of sneaking in and mining the area before drawing them out. Really any of the animals have insanely good perception, making stealth prior to rank three pretty meaningless against them. Raider types, on the other hand, can easily be snuck up on even without any ranks provided you are in mostly light armor.
Early on, the best way to tackle super mutant held areas is to pop one patroller from a long distance, then bust out the Combat Shot Gun and take out the hounds (who will find you and get there first) before disengaging. Once the hounds are dealt with, its trivial to pick apart any mutant camp with a long range stealth guy. I strongly suggest modding up at least one laser rifle or institute rifle purely for early supermutant fights, as their energy resistance kind of sucks compared to their physical resistance. Once you start getting suppressors on your guns it just gets retardedly easy to wipe them out, even indoors. Also be on the lookout for traps and alarms, as the Supermutants like to litter their camps with these (plus disarming them nets more XP gain) and walking past a tin can alarm can get the whole place on you in two seconds.
