Price. LOL.
.. and Cubase has a better midi editor of sorts.
Here's my opinion based on the fact that i'm a Nuendo guy that deals stricly with analog audio.
Nuendo has the Dolby 5.1 thing going for it.
Steinberg is selling Nuendo as a multi track workstation for movie guys (higher $) and cubase is for the strictly music guy.
I use Nuendo for stricly music. I find the user interface more intuitive and profesional for my taste. Cubase looks too square and primitive (although i only tried the demo.)
I'm sticking with the v1 Nuendo .. the new Nuendo looks too 'pretty'. Cluttered interface.
So there, that's the diff IMHO, not much help am i.