Not at all. His mind was not completely clear yet.
Flying can only be achieved by those who carry the anomaly, Neo, Smith, and Trinity. As a result, Neo can change or break certain rules of the Matrix, but Neo must have a full understanding of reality. He must believe that he's the one so that the anomaly code's is activated. Neo's believe came from Trinity and it wasn't until she kissed him in the first film that the code was activated.
After he died in Revolutions his body was reconstructed by the Analyst, but the Analyst could not reactivate the anomaly code without Trinity. The Analyst controlled Neo using stories to fill Neo's mind with doubts. He used the blue pills to suppress the code in him. The only time Neo shows abilities in Resurrections is when Neo is thinking about Trinnity or near her, hence some of his abilities manifest, but not completely. He even struggles to stop bullets compared to the OG trilogy when he was at full power.
Getting back to Resurrections, Neo has been directly manipulated and experimented on by the Analyst for decades, not to mention getting Neo hooked on the blue pills. It took time for Neo to recover, to detox. Trinity on the other hand, was not under the same level of manipulation. The Analyst used the fake family/bots to keep her in place. That's why she was able to clear her mind more easily and before Neo. Different levels of manipulation.
That's why by the end of the film Neo is back to his old self and at full power. He recovered; his mind completely adjusted. No different than people getting of drugs going through withdrawal.