Well, there has to be a reason for Vader to state in ANH: "THIS time nobody will stop us." - Perhaps the thing seen in ROTS was blown apart long before ANH.
I would also think, that the plans of the Seperatists have to be re-designed, since a Seperatist-DeathStar would be suited to their kind of equipment (droid-fighters) and highly automated (again droids), but with little facilites for millions of living beings.
SWTC Update: Saxton's rational; ROTS "Death Star"
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