Yeah. The major slow projects I can think of in recent years; Second Ave. Subway, East Side Access, Crossrail, etc. all involve deep bore tunneling through some of the most densely occupied land on Earth. Utility relocation, minimizing disruption to residents and businesses, etc. are the "hard part" here. If you could just nuke Midtown, East Side Access would have been easy. If you could demolish half of the Upper East Side, build a subway in the crater, and then cover it with new buildings, it would have been ready sooner. But, that's impractical. People are emotionally attached to their homes and neighborhoods.
That said, future projects can probably done more cheaply. IBX and QueensLink won't involve much underground work, and the right of way is already clear. The problem is that the benefit isn't clear enough to actually fund the projects and get them started. (That is an even more complicated problem. The MTA is a state body, subway lines entirely within the city are not something people on Long Island and Westchester want to pay for. Maybe there should be some sort of Independent Subway that the city itself pays for ;)
The low cost leader in subway construction is Spain and they use deep bore tunneling, and they even use larger tunnels than most everyone else (one large tunnel is more expensive than two smaller ones)
I remember when I was in Boston a discussion of how to expand one of the T-lines under Tufts Medical Center without causing vibrational problems for the equipment in the hospital right above.
That said, future projects can probably done more cheaply. IBX and QueensLink won't involve much underground work, and the right of way is already clear. The problem is that the benefit isn't clear enough to actually fund the projects and get them started. (That is an even more complicated problem. The MTA is a state body, subway lines entirely within the city are not something people on Long Island and Westchester want to pay for. Maybe there should be some sort of Independent Subway that the city itself pays for ;)