I think having new contests like this could be a cool thing and I really hope we can make it happen in a way most people will enjoy it!
I'm personally not too concerned with CCBS/System, I think that's an issue that will solve itself. If winners are decided by a vote CCBS/system using MOCs would only win if most people think that that MOC is the most fitting. If It's decided by Jury, I'm sure they would think about the design fitting the character. In some cases I think it would even be fitting for a character to look very different from other beeings.
I think custom/3D printed pieces is a more complex issue. I love all the cool 3D modeled masks that were made in the last years and I think for some characters new pieces would make a lot of sense for their masks especially.
But I agree with what Wolk said:
If a model with a 3D printed piece would be in a canon design, everyone who would like to build that character would need that piece, which puts the creator of said piece in a monopoly like position.
I'm sure a solution to this could be found, for example that all the files of the custom pieces used in the winning model have to be made public. But I don't know if 3D modelers would be fine with such a rule, I fully understand that they might want to keep their files for themselves.
Another thing I want to throw into the ring I haven't seen anybody talk about is digital models and painted pieces. Would those be ok?
Modern Lego contests often accept digital models, even if they use recolors of pieces that don't exist. Most digital programs only have a pretty limited constaction piece selection, but it could get people a chance who don't have a huge collection.