So I have a wedding cake coming up and she wants carrot cake for the bottom layer, with cream cheese icing. Has anybody done one layer using cream cheese, and the other layers using buttercream? Is there a color difference?

It does look different, and cream cheese icing is hard to smooth out well. I'd tell her that you can do cream cheese as a filling and cover the cake with a vanilla buttercream like the rest of the tiers will have, but that it won't look right if you mix and match.

i've used the decorator's cream cheese icing (in recipes) and that works great with the viva method of smoothing. regarding the color, i wonder if wilton's white-white would work for the cream cheese icing like it works on the buttercream? that way all tiers would be same white color...

I made a wedding cake and they wanted one layer of carrot cake, so I used cream cheese icing for the "filling", but frosted in my standard "Indy Debbie" buttercream (when I needed the outside to be smooth and appropriate for decorating.)
Just make sure you pipe a buttercream dam so that ivory color of the cream cheese frosting doesn't sneak out!!

So, I suggested this to the bride, and she would prefer ALL layers to be cream cheese to help match it. Obviously I need to ultimately honor her request, but does that seem a little gross - cream cheese icing on chocolate cake? Maybe I'm wrong. Anybody done this one before??

It should be okay...Chocolate is good with everything (except lemons)

I guess as long as your client is aware of the limitations that are associated with cream cheese icing, then it's up to her!
what is the theme for decorations for the cake??