Although everyone eventually get more flexible for sitting in seiza, I think that it still can be tough staying in that position for long periods of time. I know in my dojo, the only requirement is that you are in seiza to bow in and out, and if you're uncomfortable, it is acceptable to sit cross-legged. It's also considered bad manners to sit with your legs splayed out in front of you.
One story on seiza. Last year, on the last day of a week long summer camp, the guest instructor taught an hour long class on meditation at six in the morning - in seiza. After a week of practicing aikido for five classes a day, most people were pretty sore and stiff, especially early in the morning. Needless to say, the majority of people shifted between seiza and cross-legged positions during the class, except the yudansha in the first row and those folks who were exceptionally flexible and/or who had a strong tolerance for pain. One of my sempai told me that at seminars, if you're sitting in the first row, you HAVE to stay in seiza the whole time. One of the poor yudansha in the first row actually feinted during the class! Man, you should have seen everyone trying to stand up after the class, it looked like we were all crippled! In hindsight it was pretty amusing.