Did a few things never get fleshed out or did I miss them?

Okay, the deja-vu thing with the cat was only to tell the observant that a change (update, if you will) had happened to the matrix - in this case the windows were now brick and our heroes were trapped.

Morpheus taking Neo through the agent training program was just as M said - to add stress to the idea that anyone still plugged in was potentially an agent. Don't overthink it.

When Smith assimilated the Oracle he gained what she knew and that made him euphoric believing that he now had all he needed to take out Neo.

You can get into the details like Neo living in apartment 101 and Trinity watching him from 303. Did you notice who the 2 window washing guys were?

The Matrix is a good introduction to Eastern philosophy. Have fun!

to add a little bit more, since the answers people have given cover most of the answers already:

1. i think this was included to give people that immersive "what if the matrix is real" feeling - using the matrix to describe lots of different unexplained or not totally understood phenomena in our real world. same with the chat between neo and oracle about ghosts, vampires, etc. i think these were really cool additions, really helped to suspend belief.

2. woman in a red dress happens in a non-sexual way many times later on, i didn't think the sexual overtone was particularly relevant. other than it gave seque for the conversation with mouse, and the future references to her.

3. i think it is implied that the smith who infects the oracle is the main "real" smith, as opposed to the others who are more like clones / followers. and it shows the real smith as a super villain laughing at his new knowledge and power.

1. Like anyone who has access to the source, the Matrix can be changed, including Neo. However, when this happens, people connected to the matrix get alarmed by the 'disorder' and if this happens often enough, the whole thing is at risk of collapsing. That's why most people noticing the change of the matrix are either killed or an Agent takes them over. This is another reason why the Architect talks about the One threatening the system as a whole when unchecked.

2. From Morpheus' point of view, nothing should get in the way of fulfilling the prophecy. He even ditched his girlfriend, Nairobi, because of it. If Neo and Trinity dated before Neo became the one, Morpheus would have smelled the rat and told them to cut it out. It's only after Morpheus realised Neo was the one for sure, he let the couple loose on love and lust in real life, nevermind in the matrix. This is why Cypher was critical of Morpheus, by the way - because Morpheus convinced red pills that they were the one at some point, even though he himself wasn't 100% sure. When he realised they weren't the one, he simply moved on to find another.

3. Smith gained control of the Oracle, which Merovingian desperately wanted (he wanted the eyes of the Oracle, in exchange for the One). So, Smith could see the sequence of events that would lead him to take over the Matrix and beat Neo. But, as Oracle once said, Smith could never see past the choices he didn't understand. Which is why he was afraid of assimilating him initially, as this wasn't part of the vision he had with Oracles powers.

Can go on for ages but will stop here for now. Your thoughts please

3. I assumed that he was laughing at his new knowledge of The One's fate and what is going to happen to humanity. He is almost manically hateful of humanity at this point.

If he had succeeded in taking over all the human minds it would make him defacto ruler of the Matrix, or at least the equal of the Architect.

In the Animatrix a bunch of kids are playing in an abandoned building full of glitches. I think they also used the deja vu thing. It is worth a watch if you like stylized animation and the Matrix.

What do you mean fleshed out? The dejavu thing happens because the programs removed the windows trapping the characters in the building. Thats why the glitch happened.

The point of the woman in red was to show that neo can't trust any of the bluepills because they could turn in to an agent at any moment.

Smith assimilates all the memories and abilities when he duplicates himself. He can predict the future after he got the oracle. That would ofcourse change him.

Guess what date Neo's passport expires in case you didn't notice ... 🙃

In the first movie there was a "deja-vu" scene and when I first watched it, this scene seemed very important. I tried to keep track of any other moments like that, and I don't recall their being any other deja-vu moments. Was this something the producers never got around to utilizing? Or was that simply the only "glitch" they experienced?

It's possible they intended to do more with it... but I feel like maybe you might be reading too much into it.

At several points the films turn some phenomenon we all experience into a bug or feature in the story's simulation; deja vu is a hotfix, ghosts/UFOs/vampires/etc are faulty programs, that sort of thing. You could say deja vu in the first film sets up for the some of the Exiles in the second/third films.

If nothing else, deja vu is revisited in Resurrections in a more literal way.

What about the whole "woman in a the red dress" scene. Morpheus made it seem like a big thing to watch out for in the matrix was distractions related to sexual desires (love and lust). Yet it seems the only thing Neo had any attraction to throughout the whole saga, was Trinity. Was Neo simply properly trained from that moment on? Or did the producers never get around to creating some kind of Matrix enemy that distracted Neo with these desires?

Neo may have been in love with Trinity... but homie's still got eyes.

Besides, Morpheus states explicitly that Red Dress is designed to impart one of the most important lessons: anyone still plugged in is a threat.

Another big thing that never fleshed out for me was when Agent Smith "infected" the Oracle and then the "Oracle Smith" seemed to behave differently than the rest of the Smiths. "She" looked at Smith in a "I'm in charge now" look and started laughing like she had some great plan in mind. Was this simply Smith celebrating the fact that he is more powerful than ever now that he has the power of the oracle? Or was that the Oracle celebrating that she now has Smith powers and plans on using them for good? Obviously the latter is not the case because Smith ends up still using the powers for evil, but then what happened to the "Oracle Smith" anyway? Is she just apart of the crowd now and is just the same as the rest of them? I was really expecting to see a scene where Neo and Smith are fighting and Neo is losing and then suddenly "Oracle Smith" comes along and turns the tide somehow.

I feel like you read that scene dramatically differently than most.

First, it's important to recognize The Oracle is no longer in control here--Smith absorbed her, so Smith isn't The Oracle, The Oracle is part of Smith.

His reaction looked to me at first to be confusion, and the new Smith looked to be communicating confidence--they just absorbed The Oracle, meaning they now all have her sight.

The Oracle was no longer in that control at that point, but she still possibly foresaw an outcome of her absorption. It's possible she knew that her sight would influence Smith to a degree--it's not possible to "view the world without time" and not be changed at least a little bit--which is why she seemed to speak through him in Revolutions.

Lastly... we learn what happens to The Oracle after Smith is quarantined. Smith obviously didn't destroy all the people he infected, he just did what Agents do which is clone himself over them. Once he was removed, everyone infected was restored.

"Haven't seen the 4th one yet"

Don't! Just stop where you are at and don't let the Resurrections ruin it for you