I decided to do them all in different playthroughs.
Institute = fighting everyone else
A modified gauss rifle from stealth with all related perks taken and the instigating prefix can kill any enemy in the game regardless of difficulty. (yup Vertibirds too)
Heavy Synth Armor has the highest armor rating in the game but Heavy Combat armor has a shadowed mod that suits stealth characters more. (Heavy synth armor is also as its name implies HEAVY it weighs the same as heavy raider armor.)
An Explosive minigun with an accelerated barrel is death incarnate with the relevant perks.