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After watching the trilogy over and over again, why did Neo even have to fight the agents or the rogue program Smith at all?
Morpheus says this,
Neo: What are you trying to tell me? That I can dodge bullets?
Morpheus: No, Neo. I’m trying to tell you that when you’re ready, you won’t have to.
So basically Morpheus is telling Neo that he is above the general laws of the Matrix.
If The Matrix had been a stand-alone movie the statement Morpheus makes would have in-fact been true.
In the very final battle between Neo and the Agents, we see that Neo is capable of stopping bullets and goes from fighting Agent Smith 2 handed, to using a single hand, to not having to fight at all and simply jumping into him to destroy him.
The sequels retcon the idea that Neo doesn't have to fight, by giving the Agents 'upgrades', which some how allows them to actually pose a challenge to Neo. Agent Smith returns in the sequels but is free of the system control and in many ways is the Anti-Neo, which gives him the same capability to ignore the rules like Neo, thus upping the tension and forcing Neo to have to fight.
A good read is the answer to the question "How far in advance were the Matrix sequels planned?". It helps to explain that, while there where originally 3 movies planned, the awakening of Neo's true power wasn't planned to completely manifest itself until the final movie, which would have allowed Morpheus's statement to be true at the very end of the series.
Neo did not need to fight the Agents after he was convinced he was the One. Before meeting the Architect he thought the purpose of the One was basically to use his abilities to help the Zion rebels "free" more humans from the Matrix and eventually destroy it. (Helping his fellow Zion rebels is why he fought the upgraded Agents at the beginning of The Matrix Reloaded -- he was helping them escape the Matrix after the Crisis Meeting by delaying the Agents.) After his meeting with the Architect he realized that
the One was never meant to end anything...it was all another system of control.
With help from the Oracle, Neo came to realize that he needed to somehow defeat Smith in order to end the war and save humanity:
Oracle: Everything that has a beginning has an end. I see the end coming. I see the darkness spreading. I see death. And you are all that stands in his way.
Neo: Smith.
Oracle: nods Very soon he’s going to have the power to destroy this world, but I believe he won’t stop there; he can’t. He won’t stop until there’s nothing left at all.
Neo: What is he?
Oracle: He is you. Your opposite, your negative, the result of the equation trying to balance itself out.
Neo: What if I can’t stop him?
Oracle: One way or another, Neo, this war is going to end. Tonight, the future of both worlds will be in your hands… or in his.
It's clear that Neo had to fight and defeat Smith in order to end the war and save humanity both in the Matrix and in the real world (Neo had to physically fight Bane-Smith in the real world to save his physical body). With this realization, Neo made a deal with Deus Ex Machina in which the machines would honor a truce with Zion if Neo succeeded in defeating Smith (who threatened not only the humans but the machines as well):
Neo: The program Smith has grown beyond your control. Soon he will spread through this city, as he spread through the Matrix. You cannot stop him. But I can.
Deus Ex Machina: We don't need you! We need nothing!
Neo: If that's true, then I've made a mistake, and you should kill me now.
Deus Ex Machina: What do you want?
Neo: Peace.
Neo succeeded in destroying Smith by sacrificing himself, which in a way means he did not have to physically fight Smith in the end -- he only had to make the choice to fight Smith with his will.
Neo does not have to fight "normal" agents at all. He chooses to engage with some of them, as seen in the video linked by DisturbedNeo in a comment, and dispatches them quickly. We can speculate on his reasons for doing this instead of just destroying each one as he did Smith. A simple explanation is, why bother?
However, Neo does have to fight Agent Smith. Even the first time they encounter each other in Reloaded, it's obvious something unique has happened with Smith. Smith alludes to Neo's "destruction" of him as the reason for his becoming "unplugged" and able to replicate himself infinitely. This alone would give Neo pause before trying the same thing again. Smith is the one who initiates the fight, of course, and Neo ultimately escapes.
By the time of their climactic fistfight in Revolutions, Smith has possessed so many bodies that it doesn't seem likely Neo could do much of anything, no matter how above the laws of the Matrix he is. Only by becoming part of Smith and then destroying all of him at once is he able to succeed. The fistfight before that is really just a clash of wills, though Smith is convinced he can win with strength alone due to body of the Oracle he is inhabiting.
Neo not having to dodge bullets means just that he had aquired some telekinetic plus some other superpowers within the Matrix. He could stop bullets but that doesn't mean that he was invulnerable to anything else or that he would destroy sentient programs just by willing it. Some special programs armed with melee weapons (eg. Merovingian's thugs) could perhaps not only harm Neo, plus posing a hinderance or threat to whatever he was trying to do. So he had to physically fight.
It's all about understanding the code.
It's about understanding the the rules of the system.
Agents weren't as tough as they seemed, only Smith posed a real danger. Because he learned the same truth that Neo did by torchering Morpheus.
Sentinels were pawns designed to keep human's out of the system.
The gate keeper(s) weren't all knowing, this is proved through the fact that key smith couldn't see his own demise.
The Matrix really isn't the perfect system, it's keeping both connected minds and free programs from escaping. This is proved through just how much trouble the admin has to go through to keep its blog tidy.
Neo really wasn't the one, there was no mystical reasoning behind it. It was proven both through the Oracal and Sypher and Neo's own conclusion.
Neo's ascent happened regardless if he was the one or not because the element behind the nature of his rise was simply belief, this is proven in that one scene where he starts to believe.
The architect was merely a plot twist, for reality as surreal as the Matrix to be made exceptable there had to be a grand designer. Even its purpose was one of merely curiosity or along the lines of - "So how far do you think you can go?" a kind of hint to Neo chasing after the white rabbit to start with.
The Matrix is a program inside a program, no one really died or got deleted. That is the greater mystery unexplained!
An important thing overlooked in a lot of questions about things Morpheus says is that Morpheus said them. In Reloaded, it turns out Morpheus was as blinded as everybody else, following a prophecy that was just another system of control. Morpheus is admirable, but he is also flawed.
Morpheus doesn't know the extent of Neo's powers as well as The Architect, Deus Ex Machina, or even Agent Smith, who's seen it happen before.
Morpheus tells Neo he's invincible and takes it on faith that Neo will also have the faith in himself to become the fairy tale that Morpheus believes in. Morpheus is the dreamer and that's his role in the simulation, because the Oracle told him it was. His role is to find and inspire the One.
So to answer the original question, Neo has to fight the programs because he is not "able to change things within the Matrix" to the extent Morpheus believed the One could.
Essentially, Neo became GOD at the end of the first movie. He was capable of warping the fabric of reality and exposed the system for what it was en masse by flying up in a crowd of people.
However, when your protagonist is God, there is nothing that can challenge him. That doesn't work for a story.
So, faced with making sequels, the Wachowskis downgraded Neo to the level of a Superman, who can fly, fight really well and occasionally use telekinesis, but is far from omnipotent.
In the Oct. 2001 script for Reloaded (http://www.horrorlair.com/movies/the_matrix_reloaded.html) and Oct. 2000 script for Revolutions (http://www.horrorlair.com/movies/the_matrix_revolutions.html), Neo was also able to form "Chi Balls" made of energy to use against Smith and other enemies. Eg. he flings one at the Merovingian's goons before grabbing the Sai.
EDIT: An earlier version of this reply incorrectly claimed that Neo was able to use Chi Balls in the shooting scripts for the sequels. This has been corrected after another user pointed out the mistake.
