Ok, here is what I think.
Special doesn't actually make the game easier, it locks content for you. All the downsides are that you can't do some things, not that you become OP.
Strength?
You can use melee weapons effectively. Cool, it's not like you will use it at the same time with a sniper rifle, you just have the option of not svcking at it for when you feel like it. Why wait until level 250 to be good at it and not enjoy it right from the start when you feel like it and get all the dialogue options and content related with Strength? You can carry weight, again, it's just inconvinience not to, so you trade enjoyment for...balance? I don't think it's balance not being able to carry stuff.
Perception?
You can sense stuff on map, why not? It's not like having to reload a game won't happen anyway. V.A.T.S accuracy? Don't use it. It's like cheating to use a cheat anyway. Nothing gamebreaking.
Endurance?
Ok this affects the game and the difficulty and it's not about content so much. You can keep this on 1 or something, or be the stat you originally would raise or max anyway so it's a decent 5 or a 10. Again, not sprinting for a long distance is just an inconvinience.
Charisma?
Again, locks content. Why not use followers? I doubt most are using them cause they help in battle anyway, it's just for immersion etc. Why lock yourself out of dialogue in a whole playthrough? Locked content, not make things easier.
Intelligence?
Ok, this affects experience but nothing gamebreaking. It's not like being level 55 will make you that much less of a destroyer than level 50, it's purpose was to unlock content earlier.
Agility?
Again, unlocks the option to use some weapons instead of others, V.A.T.S is kind of a cheat anyway and is optional, and UNLOCKS the option to sneak. It's either or, it's not both, so it's not O.P.
Luck?
Ok that might make the game easier, so you can keep that down too or raise it like Endurance.
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In short I see cheating S.P.E.C.I.A.L as a way to save a huge amount of time in playthroughs and just use anything you feel like, but NOT OP, in one playthrough.
Like in Skyrim, being able to dual wield effectively didn't make the game harder, it just removed options from you. Why not use that armor? Not use bow? Not use spells? It's not like you'd use everything at once, and it beats the hell out of having to play the whole of Skyrim again just to unlock stuff and enjoy them.
What do you guys think?