My understanding is that at some point in the past the standard trail construction method was to pave them.
Then starting at some MORE recent point in the past it was decided that asphalt wasn't natural, or toxic, or something like that. Bottom line asphalt fell out of favor and isn't being used anymore. What's out there is being left, but when it deteriorates to the point where they do trail maintenance and rebuild a section of trail they use a method with rocks that's kind of like cobble stones. You're walking on rocks and it's slick as hell when the dirt/gravel gets on top of the rocks. It's like walking on ball bearings. You see a lot of this method on the JMT section that goes up the gully to the left/east of Nevada Fall and the upper part of the Upper Yosemite Falls trail.
The section of JMT from Happy Isles up to the first bridge, i.e. up to the 'Comfort' station, is a well deserved exception. That section of trail must be the most heavily trafficked trail in the park! I imagine they applied for and received an exemption to pave it.
I was in the park for the start of that project and it was kind of fun watching these cute Bobcat scoopers, press rollers, and pavers zipping up and down that trail. Considering how narrow that trail is where do you get equipment small enough to fit up it to pave it?