I read somewhere that there won't be a 4th Matrix. Instead, the fellas will continue the story through other formats, like games. Correct me if i'm wrong, but the Wachoskies are working with a game company now.
A few answers, from my interpretation. Smith basically took over the matrix right? Neo broke smith's code right? Smith is supposedly freed from the system, right? Now, why can he fly? Because he is not part of the system anymore. When smith was an agent, he was created by the programs. He was bounded by the rules in the programs, as he, was an entity in the program itself. His thinking was defined by the program. Until one point, where he actually "thought" for himself. In The Matrix, smith said he was getting sick of the matrix. That part was probably the turning point. Where his code got altered. Probably not a very good hypothesis, but should be ample for now.
So then Neo cut through Smith, broke his codes. Somehow, smith get reassembled. This is the missing link. It wasn't explained how smith got reassembled. Unless the programs were proficient enough to recreate the agents that they have lost. If so, smith was recreated. In the midst of it, some of neo's code got integrated with the machine's programming. So in a way, smith got "freed", because of neo. He finally develops a mind to think for himself.
The indian family was.. weird. All they explained was that every program created must have a purpose. If not they will be deleted or thrown into exile. Now, both the man and the woman were programs. If they were to create a child, won't that be the result of a program? Meaning the program created a program which doesn't have a purpose. I think this part is incongruent. Or maybe there's another story behind them.
So anyway, back to the geist of the story. My take on Neo was that he is part machine, part human. See, all humans in the real world is "made", "grown". All those holes in the back/limbs? My guess is that the program that the machines have made randomly chose a guy, neo was the unlucky fella, to contain the "routines" to lead to the series of events that will let the fellow humans think that he is the key to their survival. Neo probably didn't even know that he was the one. It was the routines in him, probably event triggered, that made him realize all those abilities he had in the matrix. Thus he was able to fly and revive people and all those whatnots in the matrix. Now how come neo can see the machines? Why, it's because since he has those "routines" that the machines have provided, the machines could have also imparted some of their codes and structures and communication methods to him. Thus he was able to see them.
Or another intepretation of the golden things he saw was actually energy. That means that neo is really the "super-being". Because the machines were fuelled by human energy, it was something neo had, and is. And maybe because neo believed in more things, he had more faith in short, he was the "super-being". He could sense the energy that provided the machines with the power. Thus he can see them gold stuffs.
Finally, on the oracle and the architect. Like waht SuRfTeC said, once smith gets deleted, all regains to their original form. So the final smith that stood out was the one that infected the oracle. Now why did the oracle-smith stand out? Because it was simply the most powerful "code" of all the smiths! Well, besides the french guy. And the chinese guy. The oracle probably had the most knowledge of how the system works. So anyway, the world was beautiful in the end. Then the oracle spoke to the architect. At that point, it seemed to me that it was a conspiracy. A conspiracy between them oracle and the architect. Here's a possible explaination: The oracle and the architect were two most powerful/knowledgable programs in the matrix. Why? Because the Oracle can forsee certain stuffs, and the architect, well he basically can see everything/everyone. So the oracle and the architect are actually "collegues", in that sense. So one day, the oracle discovered that there could be a virulent code lurking within the matrix. Smith that is. And she discuesses with the architect. Upon calculations and observations, the probability of the virulent code taking over the world was quite eminent. So they decided that someone has to erase the code. They got some random guy, neo again.. -.-. So neo is basically the tool to destroy the virus. Norton Antivirus.
Well amidst all these theories, the wachoskies could ultimately just want a great action movie