Enclaves of polytheism are unlikely. However based on my reading, there is a possibility that Christianity would not be as closely related to the Roman state and there would be a religious pluralism, with Christians and pagans coexisting. From what I understand, a large part of Roman religion was political; not only the emperors were seen as divine and deified, but also the means of government were ritualized. When Christianity became dominant and emperors became Christian, it in a large way replaced the previous role of Roman religion in power, with the emperors becoming Christian, the empire did too, even persecuting pagans and settling theological disputes. The Church much like the previous Imperial Cult was not only an important spiritual institution, but also an arm of the Roman Empire.
However, even if Christianity does not become an organized state religion (either by theological disputes keeping it apart or remaining on its more popular ascetic roots) and the Roman Empire remains pluralist I don't think Greco-Roman paganism would be dominant. First, (this is an arguable point for some, but I stand by it) Christianity was a hopeful religion compared to it: it promised life eternal, the triumph of love and a caring God. It welcomed the poor and the lower classes; something that Greco-Roman paganism did not offer, or it did in a way that was not as appealing. Second: Christianity was accessible. Anyone, of any social class or backgroud could become a Christian. It was not limited by ethnic groups or nationalities. Its theology on its most basic level was accesible, and it was open to many interpretations. And Christian worship was not limited to a priest class or a secret elite. This made it a very appealing religion, even without the backing of the Imperial state. Christianity did not became dominant because of the Roman Empire; it became dominant first, and the Empire adapted to it.
Secret cults and gnostic sects, in my opinion, could not compete against Christianity. They might remain and be influential, but in terms of followers they would form a tiny percentage. The main competitors in a pluralist Roman Empire scenario would be other universalist cults (like maybe an evolution of Mithra or Isis), ethnic religions, Zoroastrianism (though maybe it would be considered the Persian religion and thus persecuted due to the hostility between the two empires... I'm not sure) and maybe Buddhism or other foreign religions. Greco-Roman religion might be an important religion on government, philosophy and of course large populations in Greece and Rome, but if the trends that were in place during the origin of Christianity were still in place, it would be eventually become less important.