Combat speed in the Matrix is a bit weird though because despite Neo awakening his One powers at the end of the first movie he was able to treat Agent Smith like he was in slow motion but he was tagged by a group of The Merovingian's old programs from the Nightmare Matrix, the Upgraded Agents gave him some light exercise, Seraph fought equally with him and Agent Smith post-virus was able to fight him.
The Merovingian's men were on the run from the Machines, who assigned the Agents the task of deleting them, so it stands to reason that an Agent should be able to defeat one, but at the same time I guess Seraph was an outdated program who is confirmed to have defeated Agent Smith in the past, so maybe the Agents are just a step down from some old programs. The problem really comes that people like Morpheus and Trinity were able to fight the Twins (some of Merovingian's programs, so likely on par with the ones Neo fought, who themselves seemed pretty comparable to each other), an Upgraded Agent and Agent Smith post-virus, admittedly with various levels of success. I have a hard time believing that Morpheus and Trinity improved that much between the first two movies, in the first movies regular humans could fight them, albeit only as fodder. Morpheus somehow fought an Upgraded Agent, a superior to Agent Smith (could block an attack from Neo that we saw Smith couldn't, leading Neo to conclude they were Upgraded) in the second movie whereas in the first Agent Smith kicked his ass and fighting an Agent was supposed to be a suicidal, Herculean task. I suspect Agents were toned down to create fight scenes for weaker characters and Neo's combat speed was toned down to where he was at the end of the first movie where Smith was incredibly slow in comparison.
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