In this first paragraph he refers to "some writings (of Yaavetz) on practice and critical issues that the mind recoils from". The ad hominem nature of the attack makes this a difficult criticism to respond to. Certainly, the Yaavetz is extremely original and independant in Mor U' Ketziah as in all his writings but I can't understand why this should be found objectionable, since all of his positions are backed up with considerable proof. I also find it hard to understand how R' Stern who clearly was very much familiar of with the writings of the critical scholars (as his Tahaluchei haAggados attests) should suddenly find the critical writings of the Yaavetz objectionable.
In the second paragraph he accuses Yaavetz of formulating his position on Kitniyos simply in order to avoid having to receive a hechser from R' Yonosan Eibischutz (Note the point he raises that the Yaavetz is referring specifically to R' Yonosan in his statement about "excessive Chumros".) Its actually technically possible to find out if Yaavetz wrote this particular statement in his youth before the fight with R' Yonosan or later on, since in the Shachter edition, the editor writes that the Yaavetz's handwriting was small and clear in his youth and became larger and more unclear as he became older (for obvious reasons). But the argument as a whole doesn't hold any water. Here is a citation from Mor U' Ketziah 453:
The novel position of the Chacham Tzvi clearly originated during "his stay in Salonika (1676–78?) and Belgrade (1679), [where] he adopted Sephardi customs and manners and, despite his Ashkenazi origin, assumed the title "ḥakham," the Sephardi title for a rabbi, and also the name "Ashkenazi.". The Yaavetz who revered his father above all else (see Megillat Sefer) clearly inherited this view. To say as R' Yosef Zecharya does that this position was formulated to avoid having to get R' Yonosan's Hecsher is simply (B'Mechilas Kvodo) ridiculous.
On the issue of Yaavtez's strongly worded polemical statements, it would be well to take note of his statement in the Hashmota to Mor U' Ketziah 1 that in many cases he uses the language of Melitzah causing a very sharp sentence that don't really mirror his true feelings.
For more on Yaavetz's position on Kitniyos - see Maharatz Chajes's Minchas Kanaos No. 6, and Maamer Mordechai no. 32 cited in Sharei Teshuva no. 453 (couretsy of the Mahadir of the new ShuT Chcham Tzvi)
(Side note: I highly recommend Prof. Shachter's History and memory of self : the autobiography of Rabbi Jacob Emden - Jewish History and Jewish Memory which clarifies the motives behind the writing of Megillat Sefer.)
See also the Introduction to the new edition of Ishim V' Shittos (2007) wherein they write that R' Zevin went to the Chafetz Chaim to get a heter for kitniyos in a year when there was a lack of food. The CC gave it but refused to have it placed in writing.
I'd also like to provide another interesting citation from the same Teshuva in Zecher Yosef:
On the right side is the position of the Besamim Rosh (R' Saul Berlin who was the Yaavetz's great-nephew. On him I highly recommend the very insightful article of Talya Fishman, "Forging Jewish memory : "Besamim Rosh" and the invention of pre-emancipation Jewish culture - Jewish History and Jewish Memory (1998) 70-88") that the minhag of Kitniyos is actually a Karaite custom and R' Yosef Zecharia's refutation. On the left is Shir's position from which one can see how highly he was thought of by R' Stern.