The hosts began brightly with Sam Davies edging the kicking battle against opposite number Henry Slade but England ultimately had more firepower, scoring tries through Jack Nowell and Harry Wells' double.
As the second half wore on, England professionally closed out the win, leaving Wales with just five Davies penalties to show for their efforts in a 28-15 defeat.
But Wilson, whose side finished third at last year's Junior World Championship, believes there are plenty of positives to take from the performance.
"We're disappointed with the match, especially in the second half - our performance was poor," said Wilson.
"We didn't control territory or possession and we got a good lesson from them in how to get in the right areas of the park and then we struggled with their driving lineout which ultimately won them the game.
"We made some poor decisions but against some much better opposition, we'll now look forward to the Junior World Cup.
"After this loss, there's plenty to look forward to and lots of positives to take."