I remember of a episode of Juspion (a old tokusatsu show) which the enemy was able to predict and counter all of his giant robot's attack. No matter how hard he fought.
The enemy was too confident that he ended saying why his mechanical monster was so tough.
Aiga Man: Aiga moves and attacks according to my will.
Juspion: That's it!! He and the monster are the same and only!
Then Juspion invaded the cockpit of the Aiga Monster and Aiga Man's reaction was precious.
Aiga Man: Why did you came here?? I could not predict that strategy...
How I can counter-attack that assault???
Aiga Man check his computer and...
Aiga Man: No answer?!? Now what I can do???
Juspion: Plasma Blazer Sword!!
Juspion's sword become a laser blade...
Juspion: Cosmic Harley!!
Juspion applies two quick strikes in Aiga Man...
Aiga Man: Aaaaaaaaaaarghhhhhhhhh!!!
Aiga Man explodes...
Juspion returns to Daileon and observe the monster got immobile...
Juspion (on Daileon): Yes, it became just a empty shell! Now it's my chance!!
Daileon charges power and prepare the finishing blow...
Juspion (on Daileon): Daion Strike!! Release Cosmic Ray!!!
Daileon punches Aiga who explodes after falling...
Being creative is the best way which a hero can defeat a enemy who learned how to counter his attacks based in battle data.
Sharivan had to deal with a enemy like that...
Sharivan: "I can't die here... If I die, then I'll don't be able to protect the people which I love. I refuse to be defeated here!!"
Sharivan then throw his sword in the enemy who guard it, but Sharivan quickly shot with his gun at the monster where he was not guarding and is badly wonded.
Then Sharivan got his blade back and impale the enemy.
Sharivan (finishing blow): Sharivan Crash!!
I would expect Atom to use his creativity, if they know how to counter his attacks, then he should fight in away which they cannot predict.
If the enemy decide to attack first if Atom stopped attacking, then a good chance would copy their strategy:
Wait them to attack and counter.
I recall of what Change Dragon did in Changeman when he went missing and supposedly dead.
He ended up pretending to be a mysterious vigilante who gave stealth attacks which made, the enemy who was able to predict all of his moves in his normal form, helpless.
The enemy monster got confused with his strategy and got his exposed brain damaged, so he could not counter anything and was defeated.
That idea of a character pretending to be another was used in my fanfic "Red Mask".