I just saw the part of Prof. Y. S. Spiegel's article in the new Yerushaseinu relating to Otzar Yisroel. He decries the tendency to judge books by their author as opposed to what is written in them. I must say that there is one piece in Otzar Yisroel that almost justifies those who condemn it. I refer to the disgraceful entry on Ramchal where it is written - "לולא תעה בנסתרות כי אז היה למשורר גדול" (and cf. the hesped for Shadal in the next entry - but written by a different author). Otzar Yisroel was a collaborative effort (like JE - R' Eisenstein contributed there but decided to make his own because he felt that it was insufficient.) R' Chaim Hirschenson wrote many of the Halacha related articles and those are of course excellent. But it is clear that some more editorial oversight was in order.
Unfortunately, Menachem Butler's AJhistory blog in no longer online as he had a lot of information on R' Eisenstein.
(He mentions in the article the Beis Vaad that S. discussed in this post.)