The Under 18 Barclays Premier Academy league Group C leaders controlled the game from start to finish as they continued their fine form since the disappointing exit from the FA Youth Cup last month.
City have now won six of their last eight league games and are on course to win their group.
The only surprise in this game was that it took 17 minutes for the Blues to take the lead, and they did so courtesy of a half-cleared corner that was drilled home by Meppen-Walter.
The Blues continued to press but went into the break with what was a well-deserved but narrow lead.
Any concerns the visitors would get back into the game were ended within the space of ten minutes after the break.
Jordi Hiwula broke into the box but was caught by the Wednesday keeper leaving the referee no alternative but to give a penalty that Rusnak successfully converted on 56 minutes.
Then, in the 66th minute, Luke Coulson was sent sprawling in the box and again, the referee had no option but to point to the spot and Rusnak again sent the keeper the wrong way to seal an emphatic victory.
Academy manager Mark Allen said: “The boys gave a very controlled and focused performance today and I was particularly pleased with the fact we had three Under-16s players in the starting eleven.
“James Horsefield was making his debut and Angus Gunn and Ashley Smith-Brown also played so there is some real talent coming through the ranks.”