Trinity's "Death"/Architect/Neo's Choice
To a large extent, Neo's final choice that the Architect gives him is based on illusion/s. Whether or not Trinity is really alive or dead or trapped in the "Matrix" is immaterial - it is Neo's choice that is the most important factor. When the Oracle in the Park tells Neo, "You've already made the choice. Now you must understand it", she is really telling him, "Look, you already made a decision on this: there is no way in hell you're going to let Trinity die", but it is the second part of that statement that is the most important. If Neo truly understood the Choice and realized that by choosing the Right Door to save "Zion", that does not mean it "excludes" Trinity: Trinity is still a part of Zion, a part of humanity - choosing to save everyone also includes her. However, Neo feels that he has no other bond more important that Trinity and places her (a single individual) as being of greater importance that the other humans of Zion (the community). That is the flaw in the "One" and that is the reason why Neo is not yet ready to join the "Source" (be it Paradise, Perfection, Nirvana, etc... take your pick).
Also, the other concept I had with the "Trinity/Agent encounter" dreams is that, just because Neo think it is a future event or that the Architect shows it to Neo near the end, it does not necessarily mean that it occurs in the Present or Future: the Oracle states that Neo's seeing the world "without time", which Neo (and most audiences, from what I've seen) assumed to be a future event, but that may not really what she's saying at all. If you've ever read into things like the science of quantum mechanics and time physics or religions like Buddhism, Jainism, or Hinduism, Time could be viewed as being circular instead of linear and in a constant state of repetion and reincarnation where past, present, and future are both seperate and the same. So, Trinity's encounter with the Agent may have perhaps been a past event instead of a future one.
The Role of Smith
By chosing the sole connection to Trinity and ignoring the connections to humanity (deciding that she is more important than all of Zion), Neo has demonstrated that he has not truly freed his mind and that he still dependent on the "physical" connections. So, in returning to the "Matrix" Matrix, Neo has proven that he is not ready for the Source and so his existence must now be terminated and reborn. That is why only Smith remains in Neo's "Matrix" - the Source has seperated Neo from ALL connections that he may have/make, leaving only Smith as a "destroyer" for Neo. Smith's primary purpose has always been to challenge and attack Neo, but his secondary purpose (which even he is not fully aware of) is to terminate Neo's existence and restart the Matrix should Neo choose the Left Door in the end. And just as Neo has visions of Trinity's "death", Smith too is starting to have visions of "Neo's end" (hence the "I've seen this" speech at the end).
The Nature of the "Matrix"
Granted, I think it is important that people develop their own interpretations on the story and ending, but you sorta/kinda hit the nail on the head in terms of the concept I had behind the Edit.
For the original film, I did (and still do) believe that there is more than one Matrix in the film and that there are numerous "Realities" that exist in the Matrix and beyond it. At the end of Reloaded, I was thoroughly convinced that my theories were correct and that the "Zion" world was merely another Matrix built on top of the first one (in particular, Neo's new "powers" in the Zion world, which for me only made sense if you looked at that world as being another simulation, another illusion). However, by the time that Revolutions came and ended, the filmmakers more or less gave me (and the other viewers) a giant middle finger and said: "Neo has powers in the real world cause he's Jesus!" "Zion is the 'real' world, as in the same reality that we're in." "All you need is Love and Peace and Unity and Humanity and...."
Naturally, I was royally P.O.ed at the Wachoskis brothers and swore off watching the sequel films ever again (I only looked at them again when I started work on this Edit).
And regarding the final line:
After going back and forth on the issue, I think I'm just going to the leave the line in as is: extending the scene any futher kinda takes away from the mood of it and, as Commander Courage pointed out, that last line of the Oracle shows that something is different/changed from the original scene in the first film.