As I see it, Nikon realised a while ago that there wasn't much room in the Dxx series of numbers for future models. Hence, when the D40 and D60 were replaced, they started the Dxxxx series of numbers with the D3000 and D5000. The numbering of the new D3100 shows how they will probably introduce updates into those lines in the future. I see the same logic at play with the D7000 - other than the rather messy "D95", there was nowhere for them to go after the D90.
I wouldn't read too much into this regarding which "class" the D7000 fits into - I see it as a D90 but better