I have been on all the high route options and the most difficult section would be Indian pass through the the Alpine lakes, which is certainly one of my favorite areas in the Winds, but there are many favorite places to choose from. You are pretty much committed thought that section and it wouldn’t be easily done in foul weather.
Also, don’t overlook the northern end going in at Green Lakes or Dubois along the new or old glacier trail. If you are comfortable with off trail travel high above tree line the northern end of the range is truly spectacular. From Green Lakes You could head up past Slide lake taking the drainage heading SSE up to Baker Lake and follow the divide north or dropping down along Kevin lake, Hourglass, Rocking horse, past Daphne and make a big loop due north past Roaring Fork and then back west over the divide and down the CDT back to Roaring Forks and Green Lakes. If you like to see Big Horn sheep, this area will not disappoint but you will have hunters up there at that time if that is an issue for you. This is also the area where I have seen Grizzlies on two occasions, both late September early October.
You could also go south from Baker and out Tourist canyon as well, drop down to Elk park as I recall and up and over the pass to Lozier Lakes and head north over Porcupine pass and down back to Green lakes.
The options are many and each one has the opportunity to provide a very memorable trip. I am not as well traveled as Andrew, but in over 40 years of backing, I haven’t found a finer place to spend time than the Winds. Throw in no permits, no bear cans, and a good chance of solitude – especially in the less traveled northern end, and it is one of the premier areas in the lower 48 states.
It is visited more often than it used to be but compared to the Sierras it is a place where you can go several days without seeing anyone much less passing on the trail. For many years I could go on a 10-14 day trip and see no one, sometimes not even at the trail head. September is the best time, little to no bugs, relatively warm days, 50’s/60’s give or take, and cool nights, usually at freezing or so. However, be prepared for colder temps and check the forecast before you head out. I have seen it get into single digits after an early snow storm passes through up high and while one night like that isn’t too bad, several in a row could be worrysome.
Sorry, I have rambled on a bit. I also apologize for punctuation and spelling as I am working off my touch screen and have two dead thumbs, as my kids call them, having had one reattached and the other one overhauled. I am also working off memory which hasn’t been as reliable as it used to be so I may have misnamed things or gotten them a bit out or order. The best advise would be to get a map, pull up Google Earth and imagine the possibilities!