I have the series on dvd, but I've only seen the ending once. I really, really love the entire series, even though I've yet to wrap my mind around the revelations chapter. i could be horribly wrong, but here goes.
At the end, it seemed that whoever got behind the director's chair first got free reign over reality. In the reset, both Angel and Dorothy are alive, so it's safe to guess that Angel chose a reality without emnity towards R.D., but instead, one in which Roger can choose of the two humans (?) freely this time.
"Understand, Roger. This city was meant to be a stage with no memory prior to 40 years ago." This is what Big Ear told him near the end. He was an android that had knowledge of the "script," so to speak and made sure Roger kinda had an upper hand in playing his role, but never too good.
"And with pride in my heart, I turn against you." This is what Dan Dastun says when he turns on the bastard Alex Rosewater. There seem to be a lot of subtle biblical themes going on here, but I haven't really sorted them through yet. Angel, the Big's judged the pilot before action, and the number 40 being a very important amount of time in the old and new testaments, Angel and Gordon going to the 666 basement level of the "set." Maybe I'm reaching here, but I know some of it applies.
Dan Dastun's memories (or deja vu) about the girl with the balloon pops up again near the end, only this time, he actually saw himself as a lad in the movie theatre. When all's wiped out and reset, will he remember this encounter? Gordon asks Angel if she'll release memories of events that happened even before 40 years ago. This could possibly explain why Dorothy's a human in the reset.
The flashbacks of the past that Roger sees when he's deep in the ocean, they're Angel's. He see's I guess the previous incarnations of Paradigm City. He sees himself as a homeless man and as manufactured pilot for a series of Big O's. Now, when I watched this I couldn't help but recall an interview with one of the creators in which he stated that The Big O was designed as a toy first and then the series was created solely to produce that toy. The series is an homage to classic anime and mecha stuff, so I think that's why they show the "doll/robot" manufacture scene. Again, I'm stretching, but the series is so vague I can't help it.
Hour glasses through the series are a constant. A brooding sense of time almost letting the cast know their time is soon up. In Alex's megadeus (why was it pronounced "duce"), there was an hour-glass indicator in the cockpit and it levelled once FINAL STAGE Big O blasted a giant hole in him. This is when Big Venus (angel's) shows up. She's strolling through reality erasing history (resetting) with each step. Here, Roger pleads with her not to let people's memories be forgotten. Then suddenly, it ends just as it began. This time, though, we see both Angel and Dorothy alive and the ruins of a building leaning on another, to say that the final battle happened and this time, more than one person remembers. Notice Angel's smiling.
I hope I shed some light on one of my favorite series and cast of characters. That Roger, he's such a louse. :')
P.S. - Beck was suck an awsome character. heha, one of my favorite episodes was The Greatest Enemy. Beck and his goons pilot these transforming robots that take about 4 minutes to transform. I mean, the transformation sequence is everything short of grand and awesome. And after they form this giant imposing robot, Big O destroys them in one punch. I hadn't laughed so hard in the whole series. I had to pause it. This is obviously an homage to the old bandai shows like Voltron and whatever was the original series of Power Rangers. Also, it's theme is soooo bad ass. An homage to Queen's Flash Gordon them, I have to listen to this at least twice a week. Oh! Does anyone have the second soundtrak to the series? The themes through the second season are beautiful. Especially the choir theme.