Japan had double the number of carries and forced Wales to make almost 100 more tackles than the visitors.
The Brave Blossoms were the more impressive team on show, although head coach Eddie Jones avoided a couple of attempts to say that afterwards.
“The only thing anybody ever remembers is the scoreboard,” said Jones. “That tells the story and is all that matters.”
Jones has suffered previous defeats in Cardiff inflicted by superior Welsh sides and has close-up knowledge of the current squad, having played them three times this year.
“Having spoken to a few people, the big thing Wales has to look at is the development system,” said Jones.
“Coaches can only coach the players they have got and Wales for a long period of time had a strong and tough team under Warren Gatland.
“It is obvious the young players have not been developed enough or as quickly as you would like, because now you have a gap in the team.”
Jones believes Wales can return to rugby’s top table.
“There are plenty of good players in Wales,” said Jones.
“Wales is one of the traditional hotbeds of rugby in the world, albeit it’s a small country.
“If they can improve the development pathway and get that right, Wales will get its place back in rugby.”