Not an easy thing to develop certainly, but relative to the cost and level of engineering effort needed to build new subway tunnels, I'm surprised that adding transportation improvements at street-grade and then bumping the street up one level, isn't something that ever gets considered. We could run effective BRT through Manhattan, or surface light rail to solve the crosstown transportation problem.
Imagine how much easier getting from Queens and Brooklyn to the Lincoln and Holland tunnels would be by car or bus if say 39th St, Canal St moved the pedestrians to an elevated walkway. What if Times Square's tourist bottleneck could be eliminated by raising Times Square?
Anyhow, unlikely to happen probably ever, but fun thought excercise