Yes it cannot autofocus on old lenses but why do you need old lenses to begin with? They are noisy when focusing and don't focus as fast.
More FPS: Are you going to shoot sports always,? If yes then D90 is a candidate, otherwise not 
Better manual controls: In video? No, it has even more limited control in video. From a photography standpoint, it may have one or two additional buttons but none that warrant buying.
Top control display: But it doesn't have a tilt screen like the D5100 and I know your last camera did and I think it is far more useful than that tiny old screen.
Premium at the time: Exactly, it WAS premium. Not anymore.
Low Light/Sensor Size: The sensor size is exactly the same, i.e APS-C. The one in the D5100 is better by many folds, the D90 cannot match the low light performance of the D5100, plus it has better dynamic range.
All this does not mean that the D90 cannot take great pictures, but why would you buy a discontinued model that is the same price as a new model and cannot perform as well?