One of the reasons for buses during the era of streetcar conversion was that they were "flexible and could be rerouted as needed to meet demands." The reality is that urban bus routes can become politically entrenched - when an authority tries to change routes, sometimes it can generate very vocal opposition from a small number of riders to retain the existing routes. Many cities have seen this occur. Sometimes a route is retained parallel to a rail line because the bus stops more frequently, and passengers that cannot walk longer distances rally to retain the bus. Other times, riders from bus served communities resist having to change midway from bus to train, and thus lobby to keep existing routes in place.
I don't know that I'd single out one city in particular. Most larger systems have examples of both cases. It's been a while since I've lived in the Baltimore area, but I do recall that at least to the south there was a realignment of some routes (the one I remember was the 14 to Annapolis, that used to go all the way into Baltimore, was cut back to meet light rail).
Wondering if I'll see the Western Route double-tracking finished before I retire...
Photo: Melbourne W7 No. 1019 on Route 78, Bridge & Church Streets, Richmond, Victoria. 10/21/2010