This stuff Bingowings has posted about astrodroids could be a great chance to make something characteristical of the separatists. I always liked the idea of Adywan of putting some old battledroid in the Sandcrawler, it gives nostalgia and makes you feel like the galaxy hasn't yet forgotten the clone wars. That battledroid there is something that takes you back to the PT and gives consistency.

So, in line with Bingo's suggestion, why don't you establish that some specifical astrodroid (let's say the cubic-headed) were the separatists astrodroids, while the round-headed, like artoo, were the republic's? So that when you get to the OT and see them all mixed up you think "hey separatist astrodroids are civil goods now", or something like that.

There was also another idea hanged here in OT.com, it was actually gonna be in some ANH edit, of Artoo intentionally attacking the cubic headed astrodroid in the sandcrawler (the one that explodes when Luke and Owen pick it). It'd add another feeling to that idea if artoo attacked it because he recognized it as an old foe from the clone wars (unlike threepio, he's never been re-programmed)..