1night in Kyoto

We'll arrive in Kyoto in the afternoon (from Odawara), and stay one night before going back to Tokyo.

Where to stay in Kyoto for one night? Any suggestion for good ryokan?

With the limit time, any suggestion where to go in Kyoto?

For JR Rail Pass, what is the different between Ordinary Car and Green Car? What is advantage of green car?

you asked:
"For JR Rail Pass, what is the different between Ordinary Car and Green Car? What is advantage of green car? "
please ask that question in the small window right above the postings. This has been discussed many times before and there is no consensus. It is also explained in the basics about the JR pass.
Where to go in Kyoto for a few hours? Kiomizu dera temple then wander around the Gion area.
Ryokan? try www.hapanhotel.net.

With only a one night stop-over, why not just stay at the Granvia at the train station?

The train page doesn't really explain the green car system all that well.

The green car is a special car (usually in the middle of the train) that is the first class car. It has spacious forward facing seats more like those in the shinkansen. Just like in an airplane, it is a more comfortable ride than in the regular seats, but don't expect free drinks or a meal or anything as there are no services.

Costs vary by the distance you travel and you can upgrade while on the green car . When the ticket collector walks by your seat you tell him where you're going and he'll tell you how much to give him (min. 700 yen). Keep the receipt he gives you in case he forgets that you paid.

If you have a rail pass then this is the way to pay if you want to ride the green car. Otherwise, it's cheaper to buy them from the machines before entering the station.

So for rail pass holders the procedure is:

1. enter the station by flashing your rail pass at the manned entry/exits
   
2. get on the green car of the train you want
   
3. tell the ticket collector the station you are going to and pay the fee
   
4. sit back and relax

So for rail pass holders the procedure is:

1. enter the station by flashing your rail pass at the manned entry/exits
2. get on the green car of the train you want
3. tell the ticket collector the station you are going to and pay the fee
4. sit back and relax

That procedure is correct if you are riding on local trains with green cars, eg if you are riding in the Tokyo area trains with green cars (eg Tokaido Line, Shonan Shinjuku, Joban, Yokosuka etc).

It is very different procedure when riding on the Shinkansen.

On the Shinkansen green cars are reserved seating, thus you need a reservation beforehand, and if you have a Ordinary JR pass, you pay for the green seat PLUS the limited express fee, so it is more expensive.

---

There are many posts concerning the differences between a Green Pass and an Ordinary pass, I don't see what it is worth to bring up that topic again.

---

If you read all the pages and still decided to ride in the green car, it is cheaper if you purchased the Kodama Economy plan and rode in the green car of a Kodoma Shinkansen from Tokyo to Kyoto, with the plan it is cheaper then a full JR Green Pass, actually its even cheaper then a 7 day JR ordinary pass itself. The only draw back under the special fare is the Kodama train takes one our longer, and you have to reserve a day in advance.