It just occurs to me that whereas other classic DC super-heroes had declared weaknesses, Barry Allen didn't--back when there wasn't any other explanation for his powers than that the lightning accident had made him really fast. But once Mark Waid invented the Speed Force that would have given Wally (and retroactively Barry) a loophole--given that speedsters draw their power from the Speed Force, just as Green Lantern draws his from the battery of power and Superman from the yellow sun.
All a mad scientist would have to do is invent a device that cuts off Barry's connection to the Speed Force, then sell this device (call it a speed gun) on the open market to crimedom. That would give metahumans a reason for knocking over banks and jewelry stores, to raise the cash for a speed gun. Just say that all the major rogues have one of these and it explains why they get the jump on the Flash.