In the recent edition of Yeshurun, there is a rather lengthy article on R' Menashe M' Ilya by a R' Dovid Kamenetsky. As you will see in the Seforim blog post I linked above, there is a dearth of information on R' Menashe so this new addition is quite useful. (He was also discussed in a previous edition of Yeshurun).
The article is written in a very polemical style and there seems to be a bit of politics behind it. Apparently, Yehoshua Mondshine (or one of his followers) published an article in Kerem Chabad 4 (I don't have access to this but I've seen a similar article in Ohr Yisroel) denigrating the accomodating nature of the Beis Medrash of the Gra towards the Maskilim  and using R' Menashe as an example.
Kamenetsky's main fight is with R' Menashe's official biographer, Mordechai Plungian. He quotes the negative HaMaggid review cited in Seforim and relates in "oral tradition" that it was written by R' Mattisyahu Strashun (Strashun usually signed his articles Yud Beis (or something like that) according to At Bash (or something like that). He accuses Plungian of recreating R' Menashe "in his own (maskilic) image". He notes several discrepancies in his account, for example a famous statement attributed to R' Yisroel Salanter (by Louis Ginzberg "Students".. - A favorite saying of his was that the Hasidim as well as their opponents, the Mitnagdim, err the former in believing that they have leaders, the latter in maintaining that they have no need of them) is put into the mouth of R' Menashe, and some other good points.
Interestingly, Kamenetsky never mentions the other great (or not so great according to the Seforim Blog post) biography on R' Menashe which is that of Isaac Barzilay.
Kamenetsky's articles are generally very tendentious and very often resort to forced, "pilpulistic" readings of the text in order to support his views. For example, R' Menashe wrote a book Pesher Davar which is very clearly attempting some type of reconciliation between Chassidim , Misnagdim and Maskilim. For some reason Kamentsky isn't happy with this so he re-interprets the book as a theoretical fusion of the elements of Kabbalah, the sciences, etc. into one coherent worldview - not directed towards any specific groups of people.
This is a very forced reading, it is almost certain (to me) that an activist like Menashe (for ex. he had plans to reinstate the Vaad Arbah Aratzos) would have very practical concerns in mind when writing such a book (pamphlet really). Second, I really don't see how Menashe's clear statement that he seeks a "reconciliation among the Tsaddikim" and his following discussion about the various "groups" can be understood to refer to a question of forming a theoretical reconciliation of various "viewpoints" unless by "forcing an elephant through the eye of a needle" (I am quoting the Talmud, not the NT - obviously).
Another article in which Kamenetsky follows a similar pattern is in Yeshurun 8-10. There he is discussing R' Shlomo Dubno who was one of the original circle of the Biurists. At one point, Dubno broke with Mendelssohn and he later had a very close relationship with many Gedolim of that time, as the Haskamos that Kamenetsky printed attest. Kamentesky is faced with a bit of a dilemma here since Mendelssohn is the personification of the evil of Haskalah, and Dubno's association with him is a bit of a headache.
Now all the evidence (very finely laid out by Altmann in his biography of M.) suggests that the cause of the break was Mendelssohn's refusal to print Dubno's lengthy introduction. This isn't good enough for Kamentsky though so he invents a conspiracy theory according to which M. deliberately refused to print the introduction in order to push of D. who was to frum for him. D. on his part was only to happy to leave because he knew how bad M. was all along anyway. This really doesn't work to well. All the documents prior to the break show a pretty fine relationship bet. M. and D. The only statements that support Kamenetsky's assertion were those written after the break up which appear only to reflect an attempt by Dubno to retroactively justify his break.
In short, Yeshurun is a very fine journal with many good articles but rather tendentious on historical issues. (Incidentally, I was quite surprised that R' Yaakov Chaim Sofer in his "Al Seforim..) in the issue prior to this one seems not to have been aware of the existence of R' Nosson Adler of Hanover/London , the Baal Nesinah La-Ger.
 Inadvertently, Kamenetsky helped me clear up an interesting historical point. It is easily understood why the Maskilim called themselves by that name (though from a purely philological point of view it might be inappropriate (V'Hamaskilim Yizaharu in Daniel isn't referring to the "rationalists") but would did their opponents call them by a complimentary term. אבל כנראה כוונתם היה על המלה מסכילים זה מזכיר לי את כמאמר המפורסם של סטנוב "לא כל הראשונים השכילו ולא כל האחרונים הסכילו" עוד יש לפרש שהוא מלשון "שכל את ידיו" (בראשית מח, יד) והבוחר יבחר
[2 Most of Kamentsky's arguments that Menashe was essentially a Misnaggid are already presented in Barzilay's book. See the chapter on Menashe's ambivalent attitude towards Chassidim (also printed in the JQR).