Errm...yes. Anyways, back to the original topic I used to have problems with this position as well. I just started sitting in it at home for as long as possible, but I made sure to stop as soon as I started feeling pain. Do it while you watch TV, or read, or maybe even eat dinner ( ) Once I had been doing this for a few weeks I found that I had no problems with it anymore.
I just wanted to be sure that the link I provided didn't get lost in my original reply .... so do check out that Mushinkan Kendo site which also provides several other sitting/bowing/posture positions.
This might seem quite strange, but I used to train swimming, and my coach later told me that swimmers tend to develop highly flexible ankles. I was able to deal with seiza quite well the first time I tried it, maybe it was partially related to that. Try swimming
i have ligament damage in both ankles and one bad knee. sometimes i can sit in seiza for as long as i want and sometimes my knee is acting up and i can only last a few minutes. once i get up i always have to jump around and shake the numbness out of my legs. suwari waza is what really kills my knee. this may lead to me quitting aikido, as much as that sucks.
If suwari waza is causeing you that much trouble speak to your teacher about it and don't do suwari waza any more. It'd be a shame to quite just because of that one little thing. Aikido has a lot more to offer. Do you know anybody that does Kiatsu? I'm not saying it will fix the ligaments in your knee but the heat from a Kiatsu practitioners hands works wonders for loosening stiffness caused by injuary.