Yosemite has instituted a destination-specific allocation system that could be expanded and applied to great advantage. Instead of quotas being based solely on the trailhead, some permits are allocated based on first night destinations, notably Little Yosemite Valley. Certain permit holders for Happy Isles and Glacier Point THs may stay at LYV and others may not. This allows more JMT hikers at HI than might otherwise be the case. It applies in other places as well: Rae Lakes Loop permits have separate quotas for clockwise and counter-clockwise departures from Roads End.
This could be used to great advantage to clear bottlenecks for through-hikers: why should a JMT throughhiker, doing maybe 20 miles a day, and clearing Yosemite Valley immediately, be subject to the same restrictive quota as someone spending a couple of nights in Little Yosemite Valley?
Similarly, at the other end, it is extremely difficult to secure a permit for the classic South to North throughhike of the JMT due the demand of overnighters spending two or more days on the MWMT. But the through hiker is typically out of the Whitney Zone in a day, making half or less of the impact on the MWMT as the summiter in the meantime. The result is that the MWMT is packed, and the JMT is probably underused, certainly by comparison.
Paradoxically, though that's not the biggest the problem with the argument for primary reliance on TH quotas: as George points out, the farther one goes into the backcountry, generally the less the TH has any correlation with the backpacker's destination, or where she spends time in the back country. Regulating the TH has from little to no correlation to regulating the backcountry use after the first fork in the trail. The most popular THs, such as HI and WP, as popular as they are for the classic log hikes they begin, are many more times as popular for the short hikes in their immediate cininity: Half Dome, Whitney, LYV etc. The TH system, however, heavily favors the intensive use by the short-hikers over the much lower impacts of the long distance traveller. That ain't right
I would be very happy to accept certain restrictions against camping at any of the heavily used sites: LYV, Tuolomne, Trail Camp, etc, or even limited time on the heavily used trail sections, in return for surer access to the full, classic routes.
