My person reason for liking this is simple, it allows me as a player to be free instead of shackled to what decisions I want to be carried over to the next game. While that stuff is fun, it also puts a damper on things if there is say a noob trap suicide mission 2/3 through the game and you have to replay 4 times the same way to get the ending you want for your next game. In FNV I can be as nice a guy or as big an [censored] as I want. I can wage war against any faction and customize my character anyway I like him without having to think about, do I want this to be a decision for the next game.
For technical reasons why I believe Cannon Is better than Carry Over is that even in the end of a series a certain set of decisions will have to be Cannon or the story is just weaker. With Cannon you can have a rich set of decisions in the story which builds great lore (which Fallout has).
Carry over is good for things like long branching romances but in the end I feel it shackles me more than enriches my play experience.
Thoughts.