That Rail Pass travel factor brings in another element, namely the presence of two basic arrival and departure points and the fact that there's no designated space for large pieces of luggage on a Shinkansen. There's space behind the last seats in the carriage where you might be able to stash a suitcase provided no one has snaffled it already, but you're pushing your luck if you try to take two. That means if two of you arrive at Kansai or Narita with a suitcase each, you need somewhere to stash the smaller of the two when you've shifted what The Supervisor needs for the rail odyssey into Hughesy's port and shifted what's likely to be surplus to requirements for the next bit into t'other one, which then goes out to The Mother's place. There are also possible cases where the big one gets deposited in a coin locker or cloak room and the back packs get used for a day or two. So it's not just a case of pack up and go.
Anyway, the long and the short of it is that the lengthy rail leg bit needs to start and finish in Kansai or Tokyo, which is another reason for using the capital as a lunch stop if it doesn't represent a viable overnight stay on the route. It didn't last time, and it misses out again here. Maybe next time.
The next thing to consider is variety. You've got limited time, a fair bit of travelling to do and while you could, say, spend a week sitting on Shinkansen and zooming all over the place, there are interesting little local lines tucked away around the islands and one of the highlights last time around was the rail motor journey from Toyama on the west coast up to Takayama and back down to Nagoya. Similarly, you could spend the whole train trip looking as Sakura, autumn leaves, temples or gardens but even when you combine leaves and gardens (natural fit, that feller) or leaves and temples you're going to need a break to spare yourself the risk of sensory overload.
Last time the mix was old buildings and garden (Kanazawa), a heritage village and old buildings (Takayama), social call (Nagoya), trying to see Mount Fuji (Hakone), social call and temples (Kitakami) and back to base in Kansai where there was a significant temple and garden component. All of that was carried out against a backdrop of Sakura.
This time we've got a different mix, and next time will be different again.
On that variety of rail experiences it's worth remembering you can do a leg from Kagoshima at one end of the archipelago to Kansai in a comfortable day and we already know the same applies from somewhere around the north of Honshu (the main island) back to Kobe/Kansai. That means you can make a substantial shift in geographic location quickly, and you can travel comfortably from the north of Honshu to the southern end of Kyushu in two days. Given that consideration, a two week rail pass gives you time to get out into the back blocks.
So with this time dedicated to coloured leaves, we start at Kobe and head up to Kitakami. That's a day, with lunch in Tokyo and a meeting with The Translator. With the coloured leaves (hopefully) in all their glory we do a bit of exploring around the north, ending up in the bottom of Hokkaido after a train trip through a tunnel under the Tsugaru Strait.
