I've come to these conclusions after dealing with travel agencies for 2 weeks:
1. With the technology, Japan is super slow. A flight purchase cannot be done without talking to a third party. Without sites similar to Orbitz and Expedia, the process, if done by phone, may take up to 1 hour (excluding waiting time and time I spent biking to 7-11 to fax my passport). Ironically, it takes up to a week if it is done online.
2. The entire process for purchasing a ticket online, includes: a) filling out an application, b) waiting for the seat availability reply (1+ days later), c) writing an email to tell them that you are interested to reserve, d) (2+ days later) an email asking for passport information, e) a phone call. Even after that, the procedure is not complete. Note: many travel agencies do not accept credit card. In Japan, it seems that bank transfers are much more popular.
3. When the say "traditonal," they mean TRADITIONAL! The entire process, if done in the site of a travel agency, includes flipping through binders of the size of a phonebook. It follows by using the computer and making phone calls to check availability. After almost an hour, the travel agency told me what I had found out in less than 1 minute on Orbitz.
4. The school's travel agency is a rip-off. They are not any cheaper than any other travel agency in Japan. In fact, taking the wide range of promotions available outside in consideration, their prices are doubled. Also, the employees are so unintelligent that they tried to brainwash me! They couldn't believe the prices that I have found. Well, it was half their prices. So much for a student discount! They were trying to convince me that the travel agencies I have found were untrustworthy. Yet, I have found them by the most legitimate middle-person websites, JTB and Yahoo.
5. On the flip side, great customer service. Although slow, every email is written with so much honorifics that I have to read it twice. Also, you get super-personal help if reserved by phone or in person. After I got the name of 1 worker, I know she is on it! The special treatment is as if I am a VIP.
6. Forget student discount, and go JTB! JTB offers crazy promotions. Also, there are special, special promotions to Kyoto and other places for foreigners. By "special promotion," I mean a package including accomodation that is cheaper than the cheapest Shinkansen ride by itself. Exclusive free pass offers that are not available to Japanese.
This must have been one of the most memorable hardship in Japan, next to getting a cell phone here.