>>2847415 (OP)
Because way way way too many people want to do trails like the JMT every year. Limiting numbers means fewer campsites on the landscape, less bad outcomes like bad shitting and trash, less negative interactions between people fighting for space, less total impact in a fragile wilderness, and most importantly, retention of wilderness character. All of the federal land management agencies that manage wilderness have been given and injucntion to preserve wilderness character, which means limiting the number of people so that anybody can go in and actually have a wilderness experience of few to no people. Even if they wanted to allow more spots they cant.
The sections that go through the national parks are regularly patrolled by wilderness rangers. Its also the PCT so they are on it all the time to help idiots and those in need. The national forest section not so much.
The real truth is that you can make a month long trip through the high sierra that doesnt involve the jmt, but a the logistics are up to you. If you want to do the popular one for ease of use, you deserve to have to go through hurdles