I did get my rail pass exchange voucher. How essential are seat reservations, particularly for the Tokyo-Kyoto train (to on the 16th, returning on the 20th, mid-day both times)? If I do go for a non-reserved car, how do I tell which are reserved cars and which aren't?

Reservations aren't essential, but they're very easy to arrange and they cost nothing if you have a JR pass. I'd certainly recommend making reservations for any long journey that you take.

If you're using a JR pass to ride a train without a reservation and you find that the unreserved car is full, conductors should let you take an available seat in an unreserved car. However, it's best to wait until the train has left the station to attempt this. If you take an unoccupied seat in a reserved car when the train is at a station, there's a good chance that someone will show up with a reservation for that seat. Alternatively, the conductor may warn you that you're going to have to vacate the seat at the next station because someone reserved it from there.

For Shinkansen trains, information about which cars are reserved / unreserved / green is shown on the electronic displays above the platform. There are also signs at the entrances to every car that indicate reserved / non-reserved.

There are also labels on platforms (and hanging on wires above platforms) that indicate the type of car at each point on the platform. However, these can be very tricky to interpret, because many different train configurations use the same platform and you need to know which labels are associated with the train that you're about to catch.

I disagree and think that Osaka is a better hub than Kyoto; but it really depends on how long you're going to be there and what you plan to do.

Why do you feel that way?

The reserved and unreserved cars are marked in both Japanese and English, so there shouldn't be any problem.

Trains leave Tokyo for Kyoto every few minutes, starting at 6:00AM. As long as you're not in a peak travel period, reservations should be no problem. But it costs nothing to make a reservation, so just go to the reservation office in Tokyo station and tell them about what time you want to travel. (Write it down if they don't understand.)

I prefer Kyoto as a hub because you're closer to the major sights, there's plenty to do in the evenings unless you're a hardcore partyer, and it's just a more pleasant environment all around. (Osaka is even more of a concrete jungle than Tokyo.) Also, you have only one train station to deal with for day trips, as opposed to three (Shin-Osaka, Osaka-Umeda, and Nankai Namba).

I think that most people on this board tend to overrate Kyoto and knock Osaka too much. If you are going to stay for only a short while and plan to spend most of that time exploring sites in the immediate vicinity of Kyoto, then staying in Kyoto makes sense. However, if you are going to explore the entire Kansai area, Osaka is more central in location, has better rail connections, and tends to be cheaper than Kyoto.

As you are going to only spend 4 or 5 days in the Kansai area, I would recommend staying in Kyoto and spending 3 or 4 days in Kyoto proper/Uji/Kurama and maybe 1 or 2 days on day trips to Nara and Mount Hiei. Trying to pack in Osaka, Kobe, or any other places would be stretching yourself too thin.

I don't think we overrate Kyoto at all, it's just that if a Japan trip includes Tokyo (and what first Japan trip doesn't?) then Osaka is just another large city while Kyoto actually has a portion that is reasonably different from Tokyo.

Regarding Osaka's location: When I stayed in Osaka while having a JR pass, I got a bit tired of always having to shuttle over to shin-Osaka. If you have thae JR pass, Kyoto to shin-Osaka isn't that much longer than the shuttle.

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Ahhh, the never-ending debate
 

You can actually get just about anywhere of interest in Kansai on a direct train from Osaka Station or one of the various adjacent Umeda Stations. There are two lines to Kyoto, three to Kobe and Himeji, a direct train to KIX, and Nara is reachable direct from Kita-Shinchi which is a not-very-long walk to the south (completely doable underground if weather is bad). The only time you would really need to deal with Shin-Osaka is when going to/from Tokyo -- the shin-kaisoku (special rapid service) trains that JR runs from Osaka to Kyoto and Kobe are basically as fast as the Shinkansen once you count transfer times.

Sure, there is only one big train station in Kyoto... but it's pretty far from any place you would want to stay or see.

Hello again to all of you helpful people - OP here.

Here's the update:

Staying 12 days as that's what it took to get the kind of award tickets I wanted. Will be happy to change for fewer days, even with a change fee for the flights, but here's what I have:

Air Canada, Newark to Toronto to Narita, Executive First Class

Ritz Carlton Tokyo - 5 nights on Maarriott Rewards and cash upgrade to Club Level

Hyatt Regency Kyoto - 5 nights on Hyatt Points

I did an itinerary search on www.japan-guide.com and in the 12 day itinerary, they recommended finishing Kyoto and going to Hiroshima with a night in Miyajima. Then I assume I would travel back to Tokyo for the last night and travel home the next day.

So first of all, what do you all think about the suggestion? Any other recommendations? Second, if you agree, any idea of places to look into for lodging?

I can't thank you all enough - this is the reason I joined FlyerTalk so many years ago! I am constantly amazed by the generosity of strangers!

Hiroshima & Miyajima is a well trod path - with good reason. Very worthwhile overnight trip.
I think you could fly from Hiroshima to Narita on your last day and reach NRT in time for the Air Canada flight. Other suggestions would be to spend the time in Takayama, Kanazawa, up a mountain with a hot spring. In those cases, I'd squeeze that time into the itin. before Kyoto. This should allow for a not-too-long train ride from Kyoto back to NRT on the final day.
Can it be? Is that you, Blanche?

Now that is absolutely hysterical. But no, just plain Steve.

Let me push mu luck.

Just discovered the Tokyo has a Conrad hotel. I can get a very favorable redemption there and as a Diamond, I would get Club access and a possible upgrade.

My understanding is that it is more in the business area than the tourist one, tho it is not far away. As I wrote, we are currently at the Ritz but truth be told, I would rather use those Marriott points for the Ritz in NYC. Is the Conrad as special as it sounds - somewhat close to the level of the Park Hyatt?

As always, thanks!

I haven't actually stayed there, but I think Conrad's location is fine. Right next to the fish market and the Hamarikyu Gardens (both worth visiting), and walkable to Ginza or the Imperial Palace pretty easily. Shiodome and Shinbashi are business areas more than tourist areas, I guess, but still lots of fun to wander around.

I'm in the United F lounge in SFO right now waiting for my flight to Narita. Thanks for the tips.

Reservation issues with award nights at HR Kyoto. No awards for one night and they want 71,000 Yen for the night!

Considering staying two nights in Kyoto and two in Osaka (probably St Regis Osaka on points). Is that crazy? Should I just pick another hotel in Kyoto like a Westin?

They aren't that far apart from each other so go where you can stay the cheapest.....71K JPY is a bit much! ;)