We all know that only a Sanhedrin can vote conclusively on a halakha for the entire nation. Since the Sanhedrin was dismantled, the next best option was to listening to the hachamim of your locale. There were two main locales: Eretz Yisrael and Bavel. The hachamim in Eretz Yisrael had semikha and the ones in Bavel didn't, but they continued to transmit the oral tradition as they were located in one place. Neither center had jurisdiction over the other.
Historically speaking, the Bavli school survived way past the school of Eretz Yisrael and thus all of its disciples (geonim, rishonim) were educated in the Bavli methodology. They obviously knew the Yerushalmi (at least the earlier Geonim and Rishonim), but the tradition of studying the Yerushalmi wasn't on the same level as it was not regarded as "their Talmud" (I don't think they had full manuscripts of the Yerushalmi, so that combined with it not being the the Talmud of the Geonim, Yerushalmi disappeared towards middle ages).
So naturally, the Bavli mode of thinking was what survived through the centuries. However, today we have access to the Yerushalmi like never before and there is growing scholarship in it.
How can we ignore this important part of our mesorah, a mesorah that the hachamim of Bavel said they were subordinate to when both existed at the same time?
How can we claim that the rulings of the Bavli are binding on the whole nation if there was no Sanhedrin to rule conclusively? How are we to build a new Sanhedrin without access to a key part of our mesorah?