[In an earlier post, I discussed some of R' Dovid Kamenetsky's articles in Yeshurun. For some reason, a commenter was very displeased with this post. I therefore reviewed the post and the articles in question and on the whole, I stand by all I have written. But there are some points that I would like to clarify.]
In an interesting development, the Hasidic-Mitnagidic controversy which has almost entirely disappeared from the public arena in the last few decades seems to have risen again in the pages of the Haredi scholarly journals. Thus, there is a tendency among Hasidic scholars (most notably Y. Monshine) to identify the Gra and his school (and by extension Misnagdism as a whole) as Maskilim (See the articles cited in Kamenetsky's article on R' Menashe). The neo-misnagdim have not stood by idly and Kamenetsky's article in Yeshrun is to a large part in attempt to clear the Gra and his school of the "taint" of Maskilism.
Before I begin, I would like to emphasize that Rabbi Kamenetsky is a fine scholar and he has published many important documents. My only critique is that to a certain extent he allows his political agenda to influence his scholarship.
My first critique of Kamenetsky, involves his series of article in Yeshurun - 8-10, in which he attempts to lighten the association of R' Shlomo Dubno (who was connected with the Gra) and R' Moshe Mendelssohn by insisting that Dubno left because he discovered Mendelssohn's "non-kosher" philosophy. The reader is invited to examine the documents cited by A. Altmann in his biography pgs. 399 ff. It is clear from documents relating to the period of the break-up (as opposed to the documents Kamenetsky cites which were written years later) that the chief reason Dubno left was because Mendelssohn refused to publish his lengthy introduction. Kamenetsky's claim that Mendelssohn deliberately refused to publish his introdocution in order to cause Dubno - who was to frum for him - to leave has no basis and in fact contradicts all relevant documents of that period.
My second critique involved his important article on R' Menashe M' Ilya (Yeshurun 20). Previously, Prof. I. Barzilay had published a full length biography on R' Menashe (I only have access to the various articles he has published) . As Dan Rabinowitz wrote in his review at Seforim, this book is "rife with sloppy work" and is therefore not very valuable. Despite this, I believe that there is a large amount of valuable material within his book so I would have expected R' Kamenetsky to cite it at the very least. Instead, he simply insists that all Mensahe's biographers up until now were Maskilim with an "agenda".
Kamentsky engages in frequent harsh polemics against Menashe's main biographer, Mordechai Plungian. He claims that Plungian deliberately forged the majority of the biography in order to recreate R' Menashe "in his own (maskilic) image". Now, I agree with R' Kamenetsky that Plungian's work is exceedingly unreliable based as it is on hearsay and belonging as it does to the genre of literary historiography (to some degree like Mekor Baruch) in which the author takes extensive artistic license. R' Kamenetsky provides ample proof of its unreliablity. I draw the line at actual fraudulence and I don't believe evidence has been provided to support this .
First, there is a reason why Plungian chose R' Menashe as his hero and this could only be because R' Menashe's reputation as an unconventional figure was already well-known. Second, R' Menashe's protestation against those who are afraid of new thoughts and push away all those who come to investigate them  bespeaks some type of personal experience .
Regarding, the reconcilation between the three groups that is the focus of Pesher Davar. We are working with the period in which Maskilism first started to become a significant (and controversial) force, in which the Gra's conflict with the Hasidim was at its greatest height and a book is published entitled "Pesher Davar" and tries to reconciliate three groups that roughly correspond to these three groups. Any attempts to deny that Menashe was attempting a reconciliation between these three groups is like one "who swears on a tree that it is a stone" and Kamenetsky's careful exegesis , if interesting, is analogous to "he who would purify a Sheretz with a hundred and fifty kal v' chomers". R' Menashe was very much the activist (see for instance Marc Shapiros' post at Seforim for an account of R' Menashe's proto-communist ideas - even if this story is apocryphal (I believe it is - this is a famous story with many variants) , it does demonstrate R' Menashe's reputation as an unconventional thinker existed independant of Plungian. Note also his plans to reinstate the Vaad Arbah Aratzos.) and so I imagine that he had very practical intentions in mind with the publication of this pamphlet.
Some random points -
1- R' Menashe's description of the second group describes them as believers of Natural Law.
2-R' Menashe's polemics in the beginning of PD against those who claim that Philosophy and Kabbalah are the same with different terms. This view was stated most famously stated by the Rema in Torat Ha-Olah III,4 (based on R' Moshe Botarel). I did not find the specific statement that Metatron is to be identified as the Active Intellect,etc. there. It is interesting to speculate whether this relates to the Gra's polemics  against Rema (He did not see the Pardes ,etc.)
 The fact that Kamenetsky has the manuscript and that it shows that Plungian edited significantly is hardly proof. Every author does that. The fact that Plungian does not cite his sources but merely writes Shomati is also not proof. One wouldn't expect Plungian to write the equivilant of "I heard from some guy in a bar" or from "my great-aunt Yentl" and I suspect that is what his "sources" were (hence the books unreliability).
 See his description of the first group. There are other statements throughout Pesher Davar that seem to hint at some type of confrontation between R' Menashe and the more "narrow-minded" believers.
 That is why although R' Kamenetsky's arguments against Plungians report that Menashe's books were burnt seem mostly compelling, I still think that there may be some ground to the report. Interestingly, there were also false reports of Mendelssohn's Biur being burnt in Vilna (see Altmann). Something must have been behind all these reports of book-burnings?
 I believe that the discrepancies that R' Kamenesky notes are the result of R' Menashe's attempt to discuss the beliefs that lie behind these movements (note his statement in Alfei Menashe that he never mention the name of the Seforim in order to avoid embarassing the authors) and to avoid referring to specific people themselves.
 In his discussion of the Gra's famous polemic against the Rambam's philosophy in the Biur. Kamenetsky would have done well to cite J. Dienstag's "The Relation of R. Elijah Gaon to the Philosophy of Maimonides." Talpioth 4 (1949): 253-268 rather then reinventing the wheel.
[Update: The following article might have some useful information. Can anyone check this -
מרדכי פלונגיאן - דיוקן של משכיל נוסח העיר וילנה]