Using puppets was just the best way to achieve it at the time... it's not the point.
Depends on what you want to achieve and how you work... with mocap, you have actors reacting to someone who's on set, not just talking to a tennis ball in front of a green screen. The new planet of the apes movies couldn't be achieved with practical effects... Rocket Racoon would be a lot more limited too if he was just animatronic.
Yep, have them climb, jump and wreak havoc freely without having to hide them behind a kitchen counter or a couch...