As I addressed those differences in my answer to "why-is-talmud-bavli-studied-more-than-yerushalmi":
Please note that R' Yochanan and R' Yeremiya, the authors of those statements were both Israelis, so they "criticize" the way Babylonians study Torah, calling them חושך.
I personally see it not as rude criticism but as a very keen observation - indeed as the saying goes "רחוק מהעין רחוק מהלב" it appears that the Torah centers in Babylon were not only far from Eretz Israel physically but also "spiritually", feeling a great deal of freedom from the Torah of the Israeli Rabbis and their tradition.
Exile is always called חושך (compare to the Greek exile called חושך in Ber.Rabboh 2,4 "שהחשיכה עיניהם של ישראל), as opposed to the light of the Temple and Zion.
So the Israeli Rabbis call the Babylonian approach to Talmud - as Halacha learning as darkness, the lack of the divine "light" of the Wisdom of the Land of Israel.
This is well put in the WIKI page:
רבי ירמיה העריך רבות את ארץ ישראל ואת תלמודה. בכך דמה לרבו, רבי זירא, שעלה אף הוא מבבל לארץ ישראל, ומתוך חיבת הארץ ותלמודה הִרבָּה בתעניות לשכיחת תלמודה של בבל,
בשל דרך הלימוד השונה והפלפול שהיה נהוג שם.
על תלמודה של בבל אמר את הפסוק "במחשכים הושיבני כמתי עולם",
ובשומעו דבר הלכה שנאמר בבבל והיה מנוגד לדעת החכמים בארץ ישראל, היה דוחה את דבריהם באמירה: בבליים טפשים, משום שיושבים בארץ חשוּכה אומרים דברים חשוּכים.
So to your question - yes, the Israeli Rabbis saw the Babylonian approach as inferior one relatively to theirs, seeing the Babylonian scholars as stupid and rude, criticising their argumentation and reasoning, but indeed the Babylonians didn't see it as such but a different cultural phenomenon embracing the fact that the majority of the nation is scattered abroad and requires a different way of Rabbinical thinking and leadership (see my other deleted answer there).