That is mostly true, but as someone who has watched Costa Rica a lot, I must say they are pretty good at transitioning quickly through midfield on counterattacks. Anytime they had anything like that going today, Japan would immediately commit a professional foul. If constant fouling keeps you from attacking, I do not think "toothless" is the right adjective. If Japan had only been this cynical/professional 4 years ago, they would have finished off Belgium.
I agree Japan is the better team but the bottom line is you need get more goals than your opponent! Costa Rica did that but Japan didn't.