Tokyo is basically a giant blob of loosely related neighborhoods (which are each basically a city unto themselves with very distinct personalities). In all of my visits, I never find myself in the same area two days in a row (unless I am at Disney), because there are just so many interesting places to go to all over the place. The great thing is that they are all easily within reach from train. The single most important factor in choosing where to stay is the proximity to a subway station that provides good connections to everywhere else. Pretty much any stop on the Yamanote circle line is going to be close (or at least easy to reach) to wherever you want to be. Ueno and Asakusa are perfectly fine bases for a trip.