I at first found seiza hideously uncomfortable when I started taking classes. I've been getting better at it, though my ankles are a bit stiff immediately afterwards. I think that not only does practice help, but trying a variety of different variations of seiza has helped- ie, spread your legs further apart, change the position of your feet, etc. Just sit down, and spend a few minutes finding the most comfortable way to sit.
I've also noticed that women have a much easier time(in general) with sitting in seiza. Though it could be that the women I have spoken to do it habitually.
Hope this helps,