There are a lot of answers to this, but first note that Leo IX, Gregory VII, Celestine V, Pious V, Pious X, John XXIII, and John Paul II have all been canonized.

Here's some of the reasons, but it's not an exhaustive list.

First: the formal process of papal canonization did not exist before the twelfth century, so many of the early popes were already being venerated as saints for the simple reason that they were early popes. Their canonization was de facto. Additionally, the Latin sanctus does not mean "saint" in the modern sense until the ninth century; before that, it simply meant "holy person", and was often a title granted to living people. But once it began to mean "saint", people tended to assume it always had.

Second: the papacy immediately after the fall of Rome (i.e. around pope # 50) was in a great deal of disarray, with factions for and against the emperor in Constantinople, and several doctrinal schisms. Fewer popes were remembered well by enough people for their cults to form.

Third: the state of the papacy in the ninth and tenth century was fairly terrible. Lots of murders, with the seat being contested almost exclusively by Roman noble families. Not very good pope material.

Fourth: the Investiture Controversy again meant fewer uncontroversially holy people for the eleventh and twelfth centuries.

Fifth: by the thirteenth century, most popes were trained first as canon lawyers, a state of affairs that persists up to the present. This means that many of them were excellent administrators, but not particularly saintly.