Those of us who follow R' Brodt's excellent posts over at Seforim already know of his near-complete grasp of all relevant sources. This is especially true for this sefer where he even cites sources from manuscript, and from sources in Latin and Judeo-German. Also worthy of note is his impressive use of of the works of the great beki'im: Aderet, Zecher Yosef, and R' Yaakov Chaim Sofer among others is also very impressive.
The sefer represents something new in that this is the first time that I am aware of in which a traditionally-oriented sefer (openly) makes extensive use of academic studies. This greatly enhances the quality of the sefer and it is to be hoped that others will follow in his path .
Following are some comments on the sefer - perhaps I will be able to add more when I complete it.
1 - pg. 79 - R' Brodt cites a Mahari Mintz that even women went to the Mikvah on Erev Rosh HaShanah. I would suggest that this citation is only good for Northern Italy which is where Mahri Mintz lived. Regarding southern Italy R' Ovadiah M' Bartenura (the Ra'av - of the same time period) reports that even biblically ordained tevilot were neglected. See the extensive discussion in "Towards a social history of Jewish popular religion : Obadiah of Bertinoro on the Jews of Palermo" - Horowitz, Elliott Journal of Religious History 17,2
2 - pg. 139 - The Rambam's use of Yerushalmi - I would add to R' Brodt's list Chaim Tchernowitz Toledot HaPosekim Vol. 1 who discusses this at length. He even brings a list of places where he believes the Rambam relies on the Yerushalmi over the Bavli!
3 - pg. 177 -On Rashi's (and Rambam's) use of Kabbalah - See my earlier post.
4 - pg. 176 - On Yashar's Metzaref L'Chochmo - I haven't seen David Rudermans book but I will point out that the Chavas Yair definitely believed that Yashar was not being complete sincere. Note the following statement in Teshuva 210:
מסתמא יש בידך ספר בחינות הדת שביקש להדיח רבים בדף ה' ע"ב ועמד נגדו כארי נוהם הרב מהר"ר יש"ר מקנדיאה בספרו מצרף לחכמה שהאריך מאד וקיבץ כעמיר גורנה רוב דעות שקדמוהו לקרב ולא לרחק בגזירת עירין ומאמר קדישין לולי דאיהו גופי' נתן דופי בכל דבריו במ"ש...
As R' I. Twersky  notes in his "Law and Spirituality" the refernce to Modena's Ari Nohem attacking Kabbalah to describe Yashar's "defense" is no accident. (It is somewhat interesting that the Chasam Sofer quotes Yashar in a maner that makes it clear that believed he was sincere. I noticed this in his chiddushim to Shabbos and in his Responsa (likely can easily be found with DBS or Bar Ilan).
5 - pg. 52 - on additions to Ibn Ezra - see my earlier post.
 It is already well known that many traditional works make use of academic books without proper citation. In a recently published sefer on אומר דבר בשם אומרו by someone Spitz (if my memory serves) I saw a section pemitting non-citation when quoting from אינשי דלא מעלי (a notoriously "plastic" term). I have gathered many Talmudic and some later sources relating to this question but I am not as yet sure how to put them together (the clearest statement in the Posekim is that of MA OC 156:2). In any event, the very fact that the matter is looked upon so severely in secular circles is itself a reason that the matter should be forbidden. Cf. the argument of the Shoel U'Meishiv concerning copyrights - ולא תהא תורה שלימה שלנו כשיחה בטילה שלהם )
 I noticed that in one paragraph we have a reference to L. Ginzberg, R' Shaul Lieberman , G. Alon, Harav someone else, etc. !