I think Canon and Nikon really differentiated themselves when the 5D3 and D800 came out. Canon seemed to be addressing the needs of their typical users who wanted a better 5D, the main complaints being AF capabilities and better shooting performance (frame rate, build quality, etc.), they addressed these and made the near perfect 5D. Few were really complaining about IQ, though they did improve that some, particularly in the high ISO range.
Nikon stepped out with a bolder camera design, one that wasn't for their typical shooter, but has some interesting features. I know a lot of Nikon shooters who have the D800, they love it for certain things, but not for others. Resolution is king with this camera, but performance otherwise not so much. The typical complaint I hear about it is the high ISO just isn't the best, most of these users have a D3s or even D700, which they prefer for event photography. I've heard of a few who have looked at the D600, so far the comments I've heard are it looks good, but not stellar in any particular feature, just a good combination for the price. When compared to other cameras, including the 5D3, it seems to be just a little less all around, including price. You get what you pay for there.
So, is Nikon way ahead? I don't see it's possible to say that as a general statement. Nikon has no equivalent to the 5D3, nor does Canon have a D800 competitor. It depends on your needs, if the D800 is better for your needs, then Nikon is ahead for you. If the 5D3 is better for your needs, then Canon is ahead for your needs. Lenses aside, they are both great, just pick the one that suits you.