I'm surprised you found the story that jerky. Nothing in Reloaded happened out of order and less was cut than in the DeZionized edition. All story lines were left intact. When a cut was made of an idea or plot thread it was removed throughout the film to prevent confusion.
Maybe I'm too close to it and know what I did. (At least in the case of M2) I felt if nothing else it was less complicated than the original version.
Btw, I always loved the jump-starting of Trinity's heart thing. Nice fx and good symbolism to go with it. It was in fact one of the things when I watch the DZ version that I immediately wanted to put back.