I notice a lot of people dislike the idea of using Kryptonite in another Superman movie.
I for one think it is essential. Especially in an origin movie. Kryptonite is too big of a part of the Superman mythos (and American pop culture for that matter) to simply ignore.
I think the key is, you have to find a unique way to use it. I.E. Not Lex placing it infront of Superman and watching him depower. Metallo would be an interesting, new way to use it. Have his body contain the kryptonite but his body also made primarily out of lead, so it only effects Superman when he opens his chest compartment and exposes the kryptonite. Think of a fight of Superman vs. Metallo with Superman trying desperately to defeat him, but also keep him at bay so he doesn't get close enough to expose him to the kryptonite or have the opportunity to open his chest plate.
Its all a matter of how you use it.