I think this is just because most of the games are usally made in the west and targeted towards a certain demographic (mostly Europe and US). The games that are made for Japan only have more Japanese looking characters (usually but not always so please no flaming).
The stories in games are also usually inspired from literature and the stories they are taken from are generally from the west as well. Even when they are not they need to make changes to appeal to a wider audience.
If the changes are not made it takes away some of the enjoyment. I am sure that all of us have experienced it first hand, when a character does something that we would never do simply because it was not logical for us but normal or at least understandable for someone in Japan.
