September is not that much less crowded there, but somewhat. Weather is usually good, so that's a plus. Yes, there's a lot of driving in Yellowstone, but that's true no matter where you stay. Flagg is not optimal for YNP but if you wanted one base camp for both parks, it's a good location. x2 on taking the Jenny Lake loop, but only in the tow vehicle/toad, NOT with the RV. It's a one-way loop, and parking is likely to be limited there this year due to construction, but the scenery is not to be missed. Take the boat across Jenny lake to the trail to the falls (and beyond, to Inspiration Point, if you're so inclined) - definitely worth it. Enjoy!