I totally agree. I think when people talk about the new Perk system they talk about their own personal preferences rather than what is good game design. A lot of RPG elements are poor game design choices that people have just grown accustomed to. They're find for the people who are used to them but terrible for new players and expanding the base of players.
A game where you're forced to replay it repeatedly to experience all the content is not really well designed. Fallout 4 is trying to let you play the way you want to.