I'm trying to build a structure for our Japan trip in order to start booking hotels and trains. Our international ANA flights are as follows and I'm thinking 4 nights total in Tokyo and 2 nights in Kyoto.

11/4 (MON) NH950 MNL to NRT - arriving at 255 pm (4 hrs 35 mins)
11/10 (SUN) NH6452 NRT to EWR - departing at 545 pm (12 hrs 45 mins)

My questions are:

1. What's the optimal order?

Option A. 2 nights Tokyo, 2 nights Kyoto, 2 Tokyo? The good thing is I'm not putting the long train ride on the same as flights, but then I might lose some efficiency since it's easy enough to transfer on the shinkansen from the NEX train and vice versa.

Option B. 4 nights Tokyo then 2 nights Kyoto, or vice versa? The only thing is we were thinking of staying in 2 separate Tokyo hotels anyway - 2 nights in Shinjuku area and 2 nights in Ginza. Not sure if this makes sense but we read that it takes a while to travel around the city so it might save time to be stationed in one area and just explore immediate neighborhoods.

2. What's the best combination of train tickets?

Option A.
JR Narita Express - Tokyo roundtrip + 2000 Suica = 5,500
Tokyo - Kyoto roundtrip plus one day Kyoto sightseeing pass = 21,000
-Not sure if the Suica credit will be enough or we would need to buy more. Also, the special Japanican Tokyo-Kyoto package only leaves and arrives in Tokyo or Shinagawa (no Shinjuku option)

Option B.
Japan Rail Pass = 28,300
-Not sure how much we would need to use the subway in Tokyo versus just using the JR line in Tokyo. We can buy the Special 1-Day Open Ticket for 600 or Special 2-Day Open Ticket for 980.

Other considerations would be day of the week. Would Tokyo or Kyoto be better on a weekday / weekend? What about hotel prices? I assume Kyoto is busier in the weekend.

Any other observations or suggestions are welcome. Thanks!