Either way, if you're going to do major renovation, remember that Springfield goes white with snow in the "wintertime" ... it's really hard to decorate when the whole town is white and the trees are dead and the bushes are under burlap sacks. You can't tell which is which. At least, that's my experience.
But back to your question:
I dread the thought of doing, by hand, what I plan to do in my mansion area, now that I want to move much of it to SH. But that's the only area I want to change, so I'll probably not nuke.
If you DO change your mind and decide to 'nuke', and if you happen to have any garbage available, I'd put little clusters of garbage before I nuke, in general zones in your town. After a 'nuke' your pieces of garbage are right where you left them before you pushed that button.
In hindsight, I wish I had done that. After a "nuke", you're left with just a vast green expanse, which is awesome to start over, BUT I found it REALLY HARD to get my bearings. I was totally disoriented, especially since I had so much land to scroll past. If I had ANY kind of distinct marker telling me which "zone" I was in, I would have at least known where to set down my categories of buildings.
Next time, I'll put, say, a cluster of a specific kind of garbage in each "zone" to act as a marker. (Orange barrels in the factory area, broken windows in the downtown area, white barrels in the civic area, etc.) Then when I start bringing the buildings out of storage, I'd have a VAGUE idea of what goes where.
The other things that stay put are Simpson house, Krustyland shuttle and lemon tree. There might be more, but those are the ones I can think of.