The best defense against him is not being there. He has all the tools to open you up in close, but none of the tools to threaten much space or contest decent buttons at range. His D1 range is the smallest in the game significantly, and his longest mid is 15f and shorter than plenty of D3's. This of course depends on your character, but a lot of the time the best way to get an advantage vs Flash is to play not let him play to his strengths as much as possible
He will inevitably get in so some tips:
Up close, his F21 string whiffs on most characters if you block the overhead then crouch block the follow up speed punches in the string.
A lot of stuff cancelled into ex Ground Pound can be anti aired, depends on your characters AA options, test this in practice. MBB3 might be sick here as well.
His only plus on block cancel is B22 RMS iirc correctly
practice punishing Lightning Kick its tricky but good players will get it most the time if they feel it coming.
Fists is a difficult punish but whiffs a long time if you neutral jump or jump at Flash on wake up.