In Photoshop CC, I think there should be a way to choose the interpolation method (Bicubic/Bilinear/etc) for Smart Objects.
When transforming a Smart Object, the Interpolation dropdown that's there for other raster transforms should be in that Options bar.
Smart Objects are far less useful when I don't have control of this interpolation, and I find myself avoiding Smart Objects because of this issue. I find that my smart objects look overly sharpened when I downscale them.