Rashi tells us that Talmud Yerushalmi is deeper then Bavli. Why do we not regard Talmud Yerushalmi as supreme to Talmud Bavli? For example the prayer Nusach of Yerushalmi is different from that off Bavli, and yet we still use the tradition of Bavli.

There are a few reasons why in certain aspects the Bavli takes preference over the Yerushalmi. The Rif, at the end of Eruvin says that Halachic preference is given to the Bavli because it came after the Yerushlami, and the Amoraim of the Bavli were fluent in the Yerushlami and nonetheless came to there decision which differed from the Yerushlami. (Regarding the rule of "Halacha kebatrai" following the opinion of the latter within the same time period, see "Encyclopedia Talmudit" in that entry) Rav Yitchak Isaac Halevi zt"l, in Dorot Rishonim (Chap. 20) offers a historical reason. Based upon Rav shrira Gaon and Rav Hai Gaon. He says that since there were persecutions in Eretz Yisrael at the time of the compiling of the Yerushlami, the halachic discussions were ended abruptly and did not reach their complete summation. We therefore rely upon the Bavli. The Natziv, in his commentary to the Torah, Ha'amek Davar, on Shmot 34:1 makes the following novel comment in explaining why the Bavli is preferred even though the Yerushalmi is holier. He compares the two Talmuds to the first and second Luchot. Although, the first Luchot were holier since they were the handiwork of G-d, nonetheless the second Luchot are the ones which remained. Similarly, although the Yerushalmi is holier since it was written by earlier scholars and it has the merit of being written in Eretz Yisrael, nevertheless the Bavli's virtue is that it was able to guide us the darkness of the Galut where the light of Eretz Yisrael did not penetrate. The Talmudic saying in Sanhedrin 24a "He made me dwell in dark places.." This, said R. Yermiah, refers to the Babylonian Talmud", says the Natziv is not a derogatory statement about the Bavli. To the contrary, it comes to teach us that the Bavli was able to enlighten us even in the dark Galut. It should be noted, though that the Rambam showed preference to the Yerushalmi because of its virtue.(See Biurei Hagra , Orach Chaim 235:13)