"Stealth maxed, ninja maxed, sand man maxed with sneak bobblehead, all sneak magazines, and all darkened muffled armor, silenced weapons works well with double shot weapons."
You can't really sneak 2 assulttrons hanging out. Or 3 deathskull scorpions and a mythic deathclaw already in battle
I can kill them all still, but it's looking grim for future enemy levels.
Level 104 isn't really that high if you're playing it the way I do (I know I'm far from alone with this play style). Being a level 104, I saw level 103 enemies a lot (think I might of saw a 107...could of mistakened a 3 for a 7 though). It wasn't until I was a level 100 until I saw deathskulls scorpions and mythic deathclaws, so I'm not sure if every 50 levels spawns new named enemies.
"Damage is never going to scale correctly. I still do not see any way you could have explored the whole map and have done all the side quests in 90 hours."
Correct, I don't think the damage can. I have no real way of knowing what there is to uncover, but last I looked I had discovered something like 340 locations and have searched a good amount of area around each one (~100 meters) for random NPC's to give me quests or not (like the skylines woman, the traveling armorer, fake Preston, etc...). EDIT: I have also scoured almost every inch of the ocean floors. There some weird stuff down there, stuff in resemblence of Fallout 3 (Or might of been New Vegas).
Anyhow, I'll be fine unilt level 150, which at that point I might turn my eyes to Just Cause 3 (looks fun).