If you're going to hike the whole JMT then start at Happy Isles. Otherwise you're skipping the first bit. It is a surreal experience to start out the trail with thousands of other "hikers" and watch the crowds diminish more and more until you're only seeing a party every hour or so past the Half Dome turnoff.
Regarding Little Yosemite Valley vs. the "Pass Through" option on the permit, I'm still confused. I BELIEVE that with LYV you can either camp there or keep going, but with "Pass Through" you must get past the Half Dome turnoff for your first night.
In any case, I arrived in Yosemite on a Saturday evening last August, camped at the backpacker's camp, and was first in line for permits at about 5:00 AM. I got a first-come permit for LYV and hit the trail about 9:00. By noon I had chosen a campsite and was soaking my feet in the Merced. After a nap, at about 4:00 I changed my mind and headed up the trail a few more miles.
Even though I was trying to take it very easy the first day, LYV just seemed too short. If you're going to climb Half Dome I would still plan to camp past the Half Dome turnoff at the Cloud's Rest trail junction instead of LYV.
In other words go for the Pass-Through permit but don't worry if you get the LYV instead.