Well the reset theory comes to mind. Or the Angel is the director theory. Both deal with pre-event paradigm city, they just differ in how the event came to happen.
On to the father/daughter thing.
I however believe that they are blood related, as in Act 14 (ever notice how the episodes are called Acts? Like part of a play?) we see a younger Dr. Waynewright. When you look at the younger Dr. Waynewright and then at Dorothy you can see similarities in their faces. Both have the same facial structure, no other character in Big O shares a similar facial structure.
Now mind you their faces are not exactly alike, but they are exceedingly similar.
And I thought Mr. Wise's son was actually blood related?
Did I miss something?