If you don't want perks that will ruin the game, don't take perks that will ruin the game. You aren't forced to spend the points.
^This
If this was an online RPG... especially an MMORPG... all your points would be extremely valid (ok, not all, but a fair number of them)
However... this is a SINGLE PLAYER ONLY game.
YOU tailor how you want your experience.
It doesn't matter if destruction is less powerful than 2hand + heavy armor. Why? You have a thing called difficulty slider that lets you tailor your games difficulty to your preferences and loadout.
The only things that could even warrant discussion are things that make Master difficulty way to easy or beginner difficult (lol wut? zero perks could play beginner

)
If you want to loot farm and not make your own weapons that are better than anything you'll find (a valid argument) then just don't take Enchanting. (Using smithing to improve magical weapons you find I would consider valid... but then again.. the choice is YOURS!)
If you want to 1HK everything... then take the perks for it!
Make your own experience.