Stealth Sniper > That. I've played both to their maximum potential, Sniping was just the same thing but easier because I got hit less, and getting sneak-attacks off was quite a bit more common especially in maps with 6+ enemies in one spot.
-Sniping Lets you do pretty much same thing but from a much farther distance, much less perks/lvls, being able to get the headshot multiplier, being able to target suicide bomber arms, MUCH better non-vats play for those rare moments you are caught with no AP, and stay in stealth more often and easily. They are close though. THE BIGGEST difference I noticed after many hours: It deals with Assaultron Dominators MUCH easier, possibly the toughest mob in the game.
-Wounding Combat Shotgun is just on another level of broken though. Like 3 seconds to kill a Legendary Assaultron Dominator, vs. god knows how long as melee I stopped counting the seconds because he perma blocks and can't be reliably targeted in Vats or Blitz'd.
But I'll agree those setups are among the top 3 game breaking. Mostly has to do with ninja and crit banker being ludicrous for any high base damage weapon, and shotgun pellets being bugged multiplying legendary effects like crazy. If they ever fix the lame blocking system vats-blitz ninja melee might go to first place, stupid Dominators.
Get blitz and a high damage melee/unarmed weapon, use vats a lot. Build for vats. Try to stay in it as much as possible.
Get ballistic helmet/chest weave asap. (Google how, spoilers).