I can appreciate the desire to see something new, but I just feel the negativity against Zod at this point is unwarranted, whether he's the main villain or not. Sure, he may not be Joker-like status, but when it comes to Supes villains, he is one of the most recognized in terms of pop-culture, even moreso than Brainiac and Darkseid, second only to Luthor and maybe Doomsday IMO. And while he's been done once before on the big screen, that was four installments ago, so the "we've already seen him" argument doesnt hold well when you see the success of Ledger as the Joker (especially in the face of Nickelson's performance.). Two-Face is another villain reborn on-screen, welcomed with open arms. Again, I apologize for TDK reference, but when you execute a superhero movie as well as Nolan did, it's going to get referenced, especially when dealing with a movie of this potential.
I also agree with you that I'd like to see this new film distance itself from what we've already seen. Give us something new, but you don't need necessarily need a new villain. The writing, directing, and acting will take care of that. I've seen four different actors don the Bat Suit. That doesn't mean I'm tired of seeing Batman on screen Every time I see a new actor fill the suit, it's like starting with a clean slate. Now, a reboot every year would get a little excessive, but with a character like Zod who we haven't seen on the big screen for 30 years, I welcome it.