There aren't any plot holes if you're just going to create a bunch of "Makes sense" arguments for everything that doesn't fit in. First of all, Trinity's death scene lasted about 5 minutes. Now I realize that it's not a plot hole, it's just TERRIBLE movie making.
"Co-existence was chosen, by both human and machine, and they can live in harmony."
What the hell is this???? Co-exist???? So the people of Zion will just say, "OK, there are still billions of humans in the Matrix but since they subconsciously aren't choosing to leave it, we'll just let 'em be." And if they don't choose to leave, they stay batteries??? HOW IS THAT AN ENDING FOR YOU????? Now THAT seems like the movies were made for no reason to me. And how exactly did Neo change the Matrix "as he saw fit" as Morpheus described??? Morpheus also described the One as someone who would lead to the "Destruction of the Matrix...." and that obviously didn't happen either. And how about a little more explanation into why Neo's powers translated into the real world???? I realize you guys have thought about it long and hard and come up with some answer that fits the movie, but a good movie should not require meditation to figure out. That's what BOOKS are for.
"The merovingian is a good representation of a program, in that he cannot understand human feelings, cannot understand the lengths the human mind and psyche is willing to go for love."
Once again, you seem to have a completely different story in your head that you've created. The merovingian portion of Revolutions was absolutely ridiculous and consisted of "Whatever, I'm not giving you what you want. Oh, you're willing to die aren't you. Well, in that case here's what you want." I mean, the whole train thing??? Could they seriously not explain it any better than that???? It seriously felt very hollow and was not explained nearly well enough to be a coherent thought. I feel that Revolutions compounded many of the problems of Reloaded, in that: The first movie was SOOO much more intelligent in it's development of the story and use of interesting camera angles, light, judicious use of special effects, etc. Clearly the Wachowski Bros. fell in love with all of the CGI at their finger tips, and didn't stop till they'd come up with one half CGI movie and another COMPLETELY CGI movie. To me, the plot holes which ARE there aren't the worst part. It's the story and filmmaking in general. The absolute sinking of the quality between M1 and M3 is staggering, and frankly I'm still pissed over the terrible travesty that was done to the first movie.