I think that a lot of people make the time in the film where Neo and Trinity aren't around out to be longer than it is. The way it's actually shot is that there are long stretches in between cuts back to them, but it's not as if they are totally abandoned.
I can totally dig that people wanted more from Neo in the third movie, but I believe the plot says that Neo's journey is on its last leg and to simply tell that would only take half the time and make for a helluva lot less "closure" than there actually is.
So they cut it against what's happening in Zion and the more minor characters because they represent physically and immediately the greater ideological struggle that Neo is involved in, and on his way to resolve.
We have to see the cold efficiency of the machines, we have to see the awesome but ultimately futile attempt the Zionites give to defend themselves. We have to see this stuff to grasp the full resonance of what The Architect says to Neo at the end of the second film.
I watched the fight knowing that the humans would be pushed backward until they finally lost. It's a classic sequence bogged down by characters most of the audience didn't care about, and of course with some contextually unfamiliar stuff thrown around (walking tanks, 2-man bazooka units, etc etc). It's classic because it hits on a lot of the conventions I would imagine belong to a Last Stand sort of sequence, which this more or less is.
There's the gruff general, the precocious and over-eager youngster. There's even some other nice touches provided by the Wachowskis to what's usually a male-dominated affair: he has two women fighting their asses off. And no matter what anyone says about the boring and one-dimensional secondary characters, I liked Chas and I felt it when she died.
I think Ebert said something similar, too. It was an effective twist on something we were, thematically at least, familiar with.
And as for Morpheus, his presence serves the plot. I think a lot of people go into movies like these expecting the Big Name Stars to be on camera for the entire running time. That's an exaggeration, but it's pointed. There's no reason why Morpheus has to "do" anything other than what he's done. Your description of him after Reloaded is apt, G-dude. And he take second fiddle to characters who are ideologically simple (Niobe, Roland) and better prepared to act in spite of philosophical turmoil, like that which Morpheus is visibly going through.
But by the time Neo martyrs himself and the sentinels become majestic jellyfish, Morpheus leads the pack once again. It's no accident that he's the first out of the hollow, and he's the one who's most immediately aware of what he's seeing. He knows it's Neo. He weeps because his faith his healed.
And as far as the ending in the Matrix itself goes... well, that's an epilogue. It's the bookend moment. The anti-climax. It didn't need to be there, and it does feel slightly off. But how else was that exposition to take place? The Architect and The Oracle are the Gods of this universe. And they were at war. A peace accord between man and machine is a peace accord between these Gods, who are also philosophical cyphers representing several ideas (rather than one each). The Oracle is actually surrounded by two characters who are themselves cyphers, reinforcing the position she represents in contradiction to the "hard-line" machine stance.
So when I sat down and thought about what the scene meant, it didn't bother me. It was more important than how it played out on screen, and I was willing to give it some thought. So it works for me.
But the real ending is Neo's body being carted off to who-knows-where. It's the Kid declaring what's happened to the populace of Zion and it's them cheering in thoughtless reaction to the suspension of a vital threat. The Kid's delivery isn't the greatest, but it does feel honest.
Anyway. There's my long-winded 2 cents once again.
