Well, “technically” Cyber Bunny wasn’t replaced by Space Penguin, Cyber Bunny was replaced by Cyber Kitty… Kraken was rather strangely replaced by Space Penguin.
I just got the new Power Up for 2nd Edition, and it has evolution cards for both 2nd Edition Cyber Kitty and Space Penguin as well as the older Cyber Bunny and Kraken (as I have all four of these), so that was pretty cool.
I think my favorite customization of all, is the cloth/rubber game mat that sits under the original game board… I always thought the original board was just too small, and monsters “not inside” Tokyo always just kinda seemed lost… having the bigger game mat allows for a proper “Tokyo Suburbs” which gives more meaning to those monsters not yet inside Tokyo proper.