Complex sentence: Japan had held many unused fifth freedom traffic rights beyond the USA, but these were seen as being less valuable than the fifth freedom traffic rights enjoyed by US air carriers via Japan because of the higher operating costs of Japanese airlines and geographical circumstances.
Split into simpler sentences: Japan had held many unused fifth freedom traffic rights beyond the USA. However, these were seen as being less valuable than the fifth freedom traffic rights enjoyed by US air carriers via Japan, because of the higher operating costs of Japanese airlines and geographical circumstances.