Yeah, that's just it. With these clashing styles it's going to be radically different, so having an idea of what y'all would prefer would definitely streamline this for us.
If you have 2 separate stories lined up for the different styles then I'd say start with whichever you are more interested in telling. If its same story and just different levels of interaction based on art style, I'd stick with 2D. I tend to personally like more extreme things so 2D generally gets my vote as bondage and other interactions don't usually look remotely good unless your artist is extremely skilled (illusion, daz, pretty much any 3DCGI just doesn't do that stuff well without LOTS of effort).
Keep in mind people tend to also have different tastes for 2D art styles and can be much harsher towards criticism even if story is really good. So if you go 2D, expect there to be an uptick in negativity towards art styles until you get a well developed art style. Also, make sure 2D artist is able to stick around entire project (changing art styles mid game can kill it).