Idiot Savant is clearly the best perk.
Why? Because it get every other perk faster with less point investment than int 10 and because there is no level cap, leveling speed is the only thing that matters. On top of that luck has better perks than int. Luck also affects your dps while int doesn't.
Agility also has bunch of good perks but agi gets significant power boost if it gets coupled with heavy luck usage. 10mm has low ap cost, doesn't require perks to get all the mods and you can put a silencer on it.
Str has melee dmg, extra carry weight but are these really worth it when you can just be a sneaking alcoholic doing steroids all day long?
Perception and endurance are kinda bad because they lack really good perks. Lockpick is nice but unlocking stuff merely gives extra stimpaks and ammo (and ez romancing) and the player is pretty much drowning on those stuff already. Power armor kinda makes endurance pointless.
Charisma only has lone wanderer. What a joke.