1 – There are significant theological differences between different parts of the Oral Torah.. For example, Yaakov Elman has shown that the Bavli and the Yerushalmi have different attitudes regarding the question of theodicy.
2 – An essential point to any discussion of Jewish theology is the fact Jewish thought is always concentrated primarily within the exegetical form. This is as opposed to the Greeks whose thought was primarily systematic. This suggestive point was discussed at length by Yeshaya Wolfsberg in an important article in Talpiot 5 pgs. 288 ff. (see also Talpiot 6 pgs. 179 ff. - and also the article following by G. Churgin).
As is well known, Neusner is notorious for his harsh polemical articles (and books!!) against many of his colleagues and teachers . In his criticism of such well-respected figures as Prof. Saul Lieberman or R' JB Soloveitchik he harps on the fact that their major works of scholarship is in the (old-fashioned) exegetical rather then the (modern) systematic form and this reflects some type of failue on their part to engage with modern scholarship. I do not understand why Neusner considers the systematic form to be inherently stronger then the exegetical form as each accomplishes a different task.. But in any event, this has nothing to do with the conflict between the old and the new but rather, as Wolfsberg explains, with Jewish as opposed to Greek methods of thought.
 See for example “When Paradigms meet...”. Interestingly, the same people who he castigates so harshly in these later articles are praised and held up as models to emulate in his earlier articles (see his Bibliographical reflections..”). I believe the key to understanding this surprising about-face is in an article in BAR. ואכמ"ל
[Update: My thanks to Kevin for his informative comment.]