Technically you could make any of them un-cliche if you worked at it and twisted the cliche, but I feel like the first would be the easiest to work with.
The good-twin/evil-twin idea screamed “CLICHE” as soon as I read it. I don’t know if it’s actually been done a lot or if it’s just that kind of premise. Good vs. evil is a good theme, but it’s shown everywhere and different contrasts (e.g. freedom vs. safety) have more opportunities for creativity, I feel like. The whole brother-vs.-brother thing can be done well, but I’m kind of tired of seeing siblings at each other’s throats everywhere, personally. 😛
The one villain known two places might not be too bad, actually. (Thinking through it I’m pretty sure it was primarily personal opinion that discarded that one initially.) It’s been done before, but I think it could be twisted and done well.
Two villains acting for one goal most jumped out at me because you don’t ordinarily see villains working together (unless it’s less of a partnership and more of a servant/master deal). I’d be interested to see two villains working together, particularly siblings. (I don’t know if the twins thing carried over to that option or not.)