I think you are exactly right, Randy. Your point (2) I think is the telling one. Nikon doesn't refresh the entire line-up at one time (nor does any other manufacturer). Because of that, cameras at various price points are frequently of different generations, leading to apparent disparities between current models that appear adjacent in the line-up pricewise.
At some point, the D90 will disappear from the line-up. At some point other bodies will likely appear at prices above and below the D7000. Those newer bodies will have technology the D7000 doesn't -- even the lower-priced ones. That's just the nature of the technology, and trying to parse Nikon's strategy without taking into the account the age of the designs will lead to much scratching of the head!