Environmental damage can be higher in at-grade systems which require the most land to build. As for relieving congestion, where the trolleys are built at grade the system actually adds to congestion by increasing delays at intersections and requiring signals to stop existing traffic. If it's going to be expensive, at least it should be faster. But the bureaucratic system of funding seldom seems capable of funding higher service solutions. Transit planners know that the faster and more convenient transit is, the more people will use it.
People are willing to pay to get places faster.
In low density, sprawled areas like San Diego, the car is still the fastest way to get around when your choices are the slow bus or the slow trolley. The general momentum of regional plans to expand the freeway and transit systems is to load the freeways until they slow down enough to make the slow transit more usable. Adding another lane of slow traffic is not really what people want. People are willing to pay to get places faster. We need to set up systems that take advantage of this market demand and use those payments to fund higher throughput travel.