I think that the crowds thin out the closer to fall it gets. Didn’t see much traffic at all walking southbound in September on the JMT in 2005, summitting Whitney one of the first days in October. September in the Sierra is a wonderland and you will probably get to experience the first fresh snowfall of the season which, for me, equated to my all-time best day of backpacking ever.
Oh, and the bugs will not bother you in September, but you can still sleep out under the open sky most nights. Enjoy your walk!
Smack