I'd rather it be a new protagonist, that way we can see how my sweat pea was shaped by Lee's deeds from an outside source. I would also feel weird steeping into Clem's shoes after being her guide/mentor/babysitter/father.
If I was writing season 2 I would start back at the begging of the outbreak. But get the new character through the first few months durring the first episode and have them meet up with Clem at the end of episode 2. That way the User can have new baggage in hand once my adorable queen enters the picture.