Yeah, that would be something to take up with Zekrom and Polar, I think. However, in the event one type changes, you can probably just do a recolouring and all is well. Also, I'm not sure how often people will challenge for positions in the League, so I don't know how often changes will take place. I can't see it being, say, three over the course of a month, so I don't think there's too much to worry about; after the main set, you might have a new one periodically unless half the League goes inactive at some point, in which case it might be best to discontinue the League or suspend it until it's reorganized.
Also, many people won't want to be one to test others; they want to be the one to say they beat the League instead. So I have a feeling there will be more challengers than Leaders. Though former Champions can always join the League too. It's possible all 12 current Leaders could indeed be displaced!
We'll see. :)