I don't like trophies/achievements for the same reason I don't like micro-transactions. Those things start influencing game design which should be solely focused on either challenging or entertaining the player.
That said, I think Nintendo should go ahead and implement centralized trophy/achievement type system so that 3rd party port games can have better parity. I also like the social and historical appreciation value of trophies between friends.
I would want use of trophies or not to remain optional and up to each individual game rather than being a required thing to publish on that system. The reason I say this is I really do believe that trophy type things can harm certain games by either making the trophy "goal" too grindy or by declaring to the player they need to move on too early by showing 100% complete long before gamer is done having fun playing that game.