In many areas, the physical terrain in San Diego does not exactly lend itself to cutting costs when installing rail systems. The easiest lines were built first. The costs will undoubtedly go up from there, while the ridership often fails to meet hoped-for expectations. It should also be noted that due to growth, drivers will not even notice any improvement on our congested freeways even with the projected ridership. Unfortunately, the environmental benefits are exaggerated too.
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.