I never had to buy a reserved seat for the Shinkansen. There have always been plenty of non-reserved seats available. If you do buy a non-reserved ticket and sit in a reserved seat, you can either move or they will charge you the difference.

4) Shinkansen is one of the most spacious trains in Japan. You dont have to forward your baggage if you dont mind carrying it.

To pamper yourself further, you can buy some bento at the train station before boarding the train. You have more choices on food than relying on the food available on the train.

1) Should we get reserved seats to be on the Mt Fuji side of the train?
2) How many seats go across the train,i.e. is it similiar to a plane where there are 1 or 2 aisles running down the middle? We would like to be as close to a window as possible.
3) If we left Shinagawa about 9am-930am, will we be caught in a crowd of people? We wantto be in Kyoto by lunch time if possible.

http://en.wikipedia.org/wiki/T%C5%8Dkaid%C5%8D_Shinkansen
You will see Mt. Fuji between Mishima and Shin-Fuji.