I just came to this board for a tutorial on Civ 5. I'm not a PhD in East Asian history, but I've taken a number of courses on it and have read much of the reputable Asian history books that are written in English.
I agree with the previous two posters. Also some other points.
1. Colonialism, conquering: If this is important for Civ 5, why have China? Out of China's past three dynasties, only the Ming was independent. The Yuan was ruled by the Mongol invaders. The Qing was ruled by the Manchus, the "northern barbarians." The shaved head look, the queue, was forced onto the Han as a sign of submission to the Manchu people. Would you say Canada is not an independent, sovereign state because of the great influence the US has over it?
Also, Japan conquered Siam and significant parts of China during WWII as well.
2. Alphabet: Who cares? There are very few alphabets in the world. English uses a Latin alphabet, which has its roots in the Phoenician alphabet, and it also Arabic numerals. Is this a sign of American inferiority? Is Phoenicia the greatest civ for inventing an alphabet? Korea and Japan have their own native scripts that are used in addition to Chinese characters, but they aren't used by outside countries.
3. Japan's place in East Asia: Aside from the Hideoyoshi invasions, the wars it fought after the Meiji Restoration through WWII, and its economic rise that peaked in the 80s, Japan hasn't been that influential in Asia.
After the pre-Korean kingdom of Paekche was vanquished, its royal family married into the Japanese family. Many Japanese now acknowledge the roots of its culture in Paekche. From this article (Paekche is the same as Baekje):
http://english.chosun.com/site/data/html_dir/2010/09/04/2010090400223.html
"Most Japanese tourists visit the Buso Mountain Fortress, the site of Baekje's last palace, and the site of Jeongnim Temple, the center of the kingdom's Buddhist culture, where Japan's ancient temples originated," a Buyeo official said. . . . They are particularly attracted to Baekje as Japanese culture is rooted in the ancient Korean kingdom."
The NYT has published many articles in the past month or so about the decline of Japan. Short story is its economy has not grown since 1990 or so. Its industries are slowly being taken over by the Chinese, Koreans, or Americans one by one. The walkman was Japanese, but it's been replaced by the iPod. Twenty years ago, Sony or some other Japanese brand was the king of TVs, now many people buy Samsung.
I think a lot of Americans have a favorable view of Japan from all the samurai movies and such. But it's also important to remember many of the things we think of as traditionally Japanese like Emperor worship were invented by the Meiji government to control its population when it was suffering heavy casualties in the Sino-Japanese and Russo-Japanese wars in the late 1800s. There's a good English language book on this, Inventing Japan by Ian Buruma. Also samurais' weapon of choice was the bow and arrow, but swords were much more romantic for Hollywood movies.