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Determining the historical reality is one thing; deciding what to do today is a different matter. While tradition is important, it's very difficult to define its parameters. I will therefore simply share some insights and guidelines that I see as relevant.
Rav Shlomo Zalman Auerbach wrote a letter (which I have, but have unfortunately misplaced) in which he strongly rejects Prof. Yehudah Feliks' contention that lettuce rather than horseradish should be used for maror. I don't believe that this was because he disputed Feliks' evidence that lettuce was the historical reality; Rav Aharon Lichtenstein reports that Rav Shlomo Zalman told him that when Mashiach comes, many halachos will have to be changed. Rather, his point was that Judaism is as Judaism does. The living tradition is far more important than the ancient historical reality.
Contrary to what some might expect, I strongly endorse the idea behind this view. Orthodox Judaism is a traditionalist way of life, and traditionalist religions are inherently and necessarily conservative. Radical change, even if done with the best intentions and good reasons, is often destabilizing and harmful. Even if a halachah has not been unequivocally canonized, it can still be sufficiently entrenched that it becomes problematic to change. This is similar to my explanation in Sacred Monsters about why Chazal's ruling that it is permitted to kill lice on Shabbos should remain in effect despite it being based on scientific error. As to how to apply this to maror, that is more complex. I can certainly see that it is perfectly legitimate to continue using horseradish, but I don't see it as being wrong for someone to choose bitter lettuce instead.
With kezayis, however, there is no unequivocal living tradition to use an egg-sized olive. As I noted in my monograph, there have always been those, such as Rabbi Chaim of Volozhin, the Avnei Nezer and others who maintained that the kezayis is the size of an ordinary olive. Even the Chazon Ish acknowledged that this is the fundamentally correct position. It is thus an established halachic view which is merely being given greater weight in light of new discoveries of manuscripts and new data concerning olives and eggs.
What about soft versus hard matzah? I really haven't studied that case in detail, yet it seems to me that the Ashkenazi practice of using hard matzah is not based on any halachic arguments (as with the giant kezayis), but rather due to historical changes in how matzos were produced in different countries. As such, Rav Hershel Shechter's letter ruling that Ashkenazim may use soft matzah does not conflict with the aforementioned values.
There is one final important point that I want to stress. Someone told me that they were at a seder in which there were Modern Orthodox parents with their son who had gone to yeshivah in Israel and become charedi. The topic of kezayis came up, and the rest of the seder was ruined by a furious argument between parents and son about these issues. So it is apparently not "needless to say" that these issues should not cause one to lose sight of values such as shalom bayis and family unity - which is a truly important theme of seder night!
P.S.- If you haven't yet booked your chol hamoed tour at The Biblical Museum of Natural History, do it now!