I have had a week to think about it, and I have changed my mind, someone put it in light for me the other night,
Lets compare Matrix agents to Matrix Reloaded Agents
MATRIX
Smith handles Morph in the bathroom, struggles to keep hands on his neck, smith slowly pushes them away
MATRIX RELOADED
Agents dent thick steel door, ,and rip the top of a car off with one hand, we've never seen any sort of strength like this from morph
MATRIX
Smith is schooled by a single hand effort by Neo, who is standing still
MATRIX RELOADED
Three 'upgraded' agents last several minutes against Neo, where they may not have been killed but just retreated, considering we didn't hear them 'fizzle' or flash of light when they die. So they might have retreated,
Agent smith (No longer part of the matrix, and no longer part of the upgraded program) takes hundreds of them to fight Neo, and they are over paced easily, Neo didn't show that sort of 'over whelming' speed vs the first 3 agents.
MATRIX
Trinity runs from Agent, she jumps through window and survives
MATRIX RELOADED
Trinity stays and fights, starts to lose, decides to run, she is chased and killed
SOMETHING TO ADD :
Morph should have died 3 or 4 times on the truck, only character shields saved him from turning into a pancake under the truck wheels, he was beaten, he even had a sword and still lost

I completely take back everything I said about the Agents,
I am sorry