September is nice but prepare yourself for sudden snow and hunters come October. Winters are not for the squeemish. That said, I like many others hike each season with many stories to tell about each of these so-called problems. As JC mentioned, mud is certainly part of the Adirondacks. I am not a big fan of summer hiking because of crowds and heat and yes, bugs.
Nature is funny that way.
You always can and maybe should visit the western or any other part of the Adirondacks besides th High Peaks for cleaner trails. Some would say these areas are even more rustic and wild.