We’re planning a similar trip for early November too. Still can’t decide between package and free & easy, but leaning towards F&E since it gives us more time to explore at our own pace.
I’m thinking of spending one or two nights in a ryokan somewhere outside Kyoto. It’s a bit more traditional futon beds, tatami mats, onsen but it looks like a nice break from the city hotels.
Haven’t booked anything yet, still reading up on which areas are family-friendly and easy to reach by train.