That's really not entirely true. Even though the individual churches had quite a bit of de facto autonomy because of distance, there still was the recognition that there was a greater whole. Therefore, there really wasn't any "Pauline churches", which Paul himself forbade, btw.
Scholars use the designation "Pauline churches" to refer to churches founded by Paul. For Paul, the church as a whole was the corporate body of Christ. But Paul does not acknowledge any surpassing ecclesial authority in Jerusalem or Rome. He views himself as an apostle on an equal footing with Peter. in fact, in Galatians 2 we find Paul publicly rebuking Peter for his hypocrisy.
Secondly, the "chair of Peter" in Rome had a special designation, and was often referred to to help settle disputes. However, because of the scattering of churches over a relatively wide area, the power of the Bishop of Rome was quite limited. In Paul's letters, he frequently talks about "one body", thus not splintering along the lines of which apostle or appointee to follow.
Rome had no unique ecclesial authority in the first 2 centuries.
As far as he title "pope" is concerned:
Tertullian, in the early part of the second century A.D., is believed to have been the first person to apply the term Pontifex Maximus (Supreme Pontiff or Pope) to the head of the Catholic Church. /QUOTE]
No, Tertullian and his successors did not apply the title to the bishop of Rome. The title was first applied to Gratian in 360 AD. But as I said, Leo was the first to qualify as Pope.
http://www.biblicalcatholic.com/apologetics/a104.htm