They did go slightly further with phasing: if you completed the story in new DA, there was a graphical change in the zone that indicated your success.
Ooh yeah, the glowy runes on the red war walls. That was a nice touch. Simple in appearance but it really made you feel like you'd accomplished something every time you saw it. Like Matthew Habashy in Atlas Park... after you saved his wife, she would be standing beside him outside City Hall.
I guess that' ssomething I'd change then. More little touches like that. They wouldn't need to affect gameplay, just have a visual and storyline impact. Little reminders, every time you passed, of the difference you were making in the city. "This is MY city. I protect (own) it. If you want to mess with this city, you go through ME."
Okay, one other thing I'd do is change the spawning code for open zones a bit. Each different neighbourhood within the zone would have a silent counter for the different enemy groups within it, and when one group's counter reached a certain number defeated, that neighbourhood would spawn a lot less of that group, and a lot more of other groups. For example, in the places where Council and Fifth Column were fighting, if the players took out enough of one side the balance of power would shift and the other side would replace the defeated side's spawns. After a while it would switch back to an even mix, but for a while you'd really see one group thriving because their competition had been eliminated. That difference might even trigger zone events like Hellion arsons and Troll raves. (*hits preview, and snickers at the term "unicorn raves"*)
I'd also tie the radio/newspaper missions to those counters. The heavier the presence a group has in that zone, the more often that group comes up in the list of available random missions.