Everyone's powers were fluctuating throughout the story though. Like Superman, the Flash and Scorpion's powers were weaker around the beginning (hence why Superman had such trouble with Sub-zero, and why Batman beat characters normally stronger than him), but on Apokolips, they were back to full power, and Scorpion & the other MK characters became stronger than ever (due to the near-complete merging of the universes), and thus were able to fully compete with the DC characters.
In short, a super amplified Scorpion fought Wally at full power which ended up in a draw.