Hmm - I would agree with you on there being some super OP and super useless perks / stats. 

Luck can definitely get insane by basically giving endless criticals and AP. 

I might give the edge to Agility at the 1 spot, mostly because of the multipliers embedded in sneak/sandman/ninja. 

I would take a small issue with trashing Charisma...but you basically have to go all in - pacify/incite/command with the three perks and pair it with sneak to make sure you actually get them to proc. Which isn't a strong case I know, but it is fun to make a Deathclaw go ham on raiders. 

I think STR might be underrated, but it depends on your character. If you are running melee or Survival mode, STR can be super helpful. 

Last note is my personal worst rated SPECIAL stat - END. You actually don't want or need one perk in there. 

So:

AGI
LUCK
STR
PER
INT
CHR
END

On STR in SM - it makes carry weight bearable. Although, as you point out Lone Wanderer is great, and will do that plus help with damage resistance and damage output. 

PER is odd- I love Demo expert, probably my favorite accesory perk. The arc and bonus damage is so helpful for so many characters. but the rest of the tree...idk, outside of a pure sniper / accuracy build, not really necessary. 

I get what you're saying about aquagirl...but rads are not really that big of an issue. Everytime I go to Spectacle Island, I pop a RADx swim across and then pop a radaway. I always have like 30 of them by level 20 anyway. Do you mean - swimming uderwater without worrying about breath?

Ah I see - yes I can get behind a more health points/less sickness combo for Smode...but really only for Smode. I will say - to your point about Adamantium S...I remember prioritizing it in my Greaser build and feeling like it helped survivability immensely during close quarters. It also seems to really take the edge off of the notrisouly dangerous explosive damage.

The last thing I'll note are some of my fav / most OP combinations:

1. Commando + Demo Expert + Spray n Pray or Kiloton Rifle for absolute explosive mayhem

2. Sneak/Blitz + Big Leagues + melee attacks for appearing out of thin air to cut throats

3. High Luck (Crit Bank, Grim Reaper's, 4 leaf clover) + Sniper for endless critical headhsots

Oh speaking of Sniper - the knock down affect of rank 2 is absurb. Very underated - I hardly see anyone talk about it. But any scoped non-auto rifle absolutely stun locks the hell out almost everything. 

I'd say penetrator in perception is a godsend when dealing with enemies in power armor, especially on survival. Although I probably wouldn't go putting 9 points into perception unless I was there for other things.

My ranking would have to be:

Luck

Agility

Intelligence

Charisma

Perception

Endurance

Strength

Luck because as has been said the criticals are insane. And to add onto that idiot savant and the first too perks which cause you to find more caps and ammo are pretty nice. Then agility for the sneak and damage bonuses and moving target which the 3rd rank is great on survival since you can sprint way longer and you tend to be doing a lot of that.

Intelligence is great because of the boost to exp, but also since all of it's perks are useful in some way.

I have charisma at 4th because of the following perks: Local Leader, Party Girl/Boy, Lone Wanderer and Cap Collector. Local leader might not be that great if you aren't interested in settlement building but when you are or you're playing survival the supply lines and personal clinics and stores are great. Party Girl, means no more getting addicted to alcohol and bonus luck. Lone Wanderer has already been explained and cap collector is self explanetory. I might also throw in Attack Dog since it can be useful.

Perception is great on one type of character with a few exceptions such as penetrator, but it isn't worth it on melee or close range characters.

Endurance has some nice perks and is only above strength because of Chem Resistance, Aquagirl/boy and Adamantine Skeleton. Although the last two do become redundant if you're using power armor.

Strength is last because at most you only really need four points into it, to get the crafting perks and in doing so you also gain access to the two melee damage perks. Sure it increases your carry weight and melee damage, but it gets overridden by the boost from power armor and on higher difficulties and survival power armor is almost necessary for melee characters (at least my own) so your better off putting points into other stats. Sure Strong Back can be useful, but if you're becoming over encumbered so frequently that you need it you might have a problem. The rest of the perks can be nice for very specific builds but to most characters they're unnecessary.

You bring up a good point GF - Power Armor negates a bunch of perks...It's one of the reasons I've played less PA builds. I almost feel like it's too powerful.

I too agree with CHR if planning on running Survival (at least to Local Leader). 

And - I freaking love Party boy/girl for melee builds (to benefit from double strength without perking strength past Blacksmith - as you noted).