Two interesting articles on the controversies (Karaites, Reformers, and, strangely, even among traditionalists) surrounding Yom Tov Sheini are - Hirsch Jakob Zimmels, "The Controversy about the Second Day of the Festival," in Samuel Belkin, ed., Abraham Weiss Jubilee Volume (New York, 1964), 139-168, and Jacob Katz, "The Orthodox Defense of the Second Day of the Festivals," Divine Law in Human Hands: Case Studies in Halakhic Flexibility (Jerusalem: Hebrew University Magnes Press, 1998), 255-319 (My thanks to Menachem Butler for telling me about these).
In the recent volume of the journal (אלול תשס"ח) Nezer HaTorah, several letters of R' Yaakov Schorr (wiki is excellent but see the intro to Mishnas R' Yaakov by Tzvi Michelson) to Rav Dr. Chanoch Ehrentrau (wiki on grandson only)  were published. In one of them he castigates R' Ehrentrau for offering a "strange and impossible explanation" of Beitzah 4b on Yom Tov Shein (that it refers to the time in which Kiddush HaChodesh was through testimony) which opens a door to those who want to abrogate it, etc.
 There are fascinating letters from both of these great Geonim in Parnes L' Doro. See eg. in letter 108 - he has a fascinating chiddush that the Bavli cites Mishnayos from those Mesechtos for which there are no Gemara in order to explicate them. (See more recently Y. Sussmans studies of the sugyos of the Bavli conecrning Zeraim and Taharos in Mechkarei Talmud 3) Schorr was very much the critical scholar. See for example his Mishnas R' Yaakov on the Tosefta and its relation to the Bavli (see more recently Y. Elman's doctoral dissertation).
From R' Ehrentrau we have a fascinating explanation of the machlokos in Pesachim 53a concerning the ripening of olives. Based on Josephus and Gesenius, he shows that each of Tanna was explaining based on his specific geographical location. We also have a lengthy mathematical exposition on the shiur of revi'is acccording to Tosafos. Parnes L' Doro is a fascinating intellectual treasure house for 19th-20th century Rabbis and a must-have for anyone interested in the subject.