The US military's bases in Okinawa comprise one of the most important issues likely to affect the US-Japan relationship. Okinawa is often viewed as one of the poorer and lesser-developed areas of Japan.
Little wonder then that some questioned the wisdom of putting a new research university there because of the huge expense and the location's remoteness. We covered this story here at Japan HEO here.
Some argue that it's the US military's presence that continues to hold Okinawa back. It certainly uses a lot of the best land and negatively impacts civilian commercial development, tourism and agriculture.
When I visited Okinawa, my impressions were that they were culturally distinct from mainstream Japanese culture (but not backward) and that they were unfairly burdened with hosting the enormous US military bases (which are mostly there to position US power closer to two hot zones: China-Taiwan, North Korea-South Korea).
See this Financial Times' report for more background on the Okinawa base issue.