I can't speak for the Nuke, but first run's are just that, the first edition printing of a disc, although at times the modification can be different from mold to mold, first run is generally considered to be more valuable, because they haven't been tweaked yet.
Valkyries are a prime examples of molds, 1st-5th mold all do different things from the CE line, so much so that you can see the differences when people sell them, and what they are used for.
I prefer the 1st run APX over the current model (titanic by DGA for those that don't think that it is still made) just as I prefer the QMS by millennium over the SMS or the Aurora MS prior to the Q plastic. So you can find some runs that are better than others, and it becomes a personal choice (I really DISLIKE the swirl APX for example).
Discraft is in my mind much better at quality control, so that the tweaking is less noticeable than with Innova. I think that Jay Rivard summed it best once to me, Innova is like Red Wine, you may have a few batches that go to vinegar, but you also end up with some fine wine (good discs), and Discraft is like White Wine, you know it works, it's typically consistent, and you don't see very many surprises.