Stations are still major places where many Japanese gather. JR are operating in 46 of 47 prefectures in Japan, except in Okinawa. Therefore renewal of the stations are commenced nationwide.
Station is not the place where people take the trains. It is a very important place to dine and do shopping. There are many Japanese stores which are located only inside the station. These stores are mainly selling foods. Either to dine at the station or for take away.
The distinguished culture of Japan is the take away. Although taking away a meal from restaurant is common in Europe, there are stores in Japan which accepts take away only. Usually these stores are small, just has a counter with display of the meal/food and you order and pay at the counter.
Usually the people in Europe buy the meal or food at the station to eat inside the train or at the station, but there are many Japanese who take the meal or food to their home or to their destinations.
In Europe, the food will be mostly self-consumed by the purchaser but Japanese buy the food as the souvenir, bringing to their friends, colleagues or even to the company which they have the appointments,
Therefore no worries in case you arrived at the station too early. You can spend the time looking at the interesting, delicious foods at the stores. If you stay nearby these large terminal stations, you can buy your meal there. However, these stores are usually located beyond the turnstiles(ticket gate) , therefore please bring your Japan Rail Pass with you.