For example, Heavy Armor perk, Fist of Steel, it is a waste perk for anyone who wear heavy armor and using weapon. The player wasting one level up to pick that to get Cushioned and Conditioning. It should be separated from the branch
Another one is Backstab in Sneak, it only benefit the one who use dagger, it is wasted perk for Archers who don't want to use dagger in sneak attack, it should be separated from the branch. The archer player wasting one level up to pick that to get Deadly Aim. Dagger backstabber player wasting one level up picking Deadly Aim to get Assassin Blade
Some perks are perfectly separated from the main branch for certain type of game-play like Dual Fury in One Handed and Dual Casting in magic, so for the one who favor these can choose a special branch in the tree.
Why some are forced upon the player while some others are not? Perk point is expensive commodity in this game because we only have one in each level up, to have some we not used but have to pick it to get the higher level we want to use is a waste