It takes time. After a few months you will get used to it. I haven't done any aikido for a year so its difficult for me to sit in seiza now. Keep in mind I am also living in Japan! Actually most Japanese hate sitting in seiza. They usually sit cross legged when in izakaya or traditional restaurants. Also there is a belief here that sitting in seiza for too long causes people, especially girls, to develop fat ugly legs.
Aikido seiza isn't so bad. Try Iaido. Iai has many kneeling and half kneeling stances which you have to jump or move around quickly from. Good leg strengthening exercise though!