Salve Aureli
What you describe of the Romans was quite true. Through the evocatio Romans invited foreign gods to Rome, adopting some gods of other nations into their own pantheon. That however is not quite what syncretism means. In early Rome distinctions were maintained between the Roman gods and those of foreign deities. I would argue that Juno Regina of Veii is not the same goddess as Juno Capitolina, any more than Carthaginian Tanit, as Juno Caelestis, could be taken to be the same goddess as Roman Juno. Etruscan Uni is related to Astarte while Roman Juno can be more closely identified with Ceres. The fact that the temple of Juno Regina of Veii was placed on the Aventine, outside the pomerium, shows that the Romans distinguished between Her and that of their own Juno. The same is seen with some other deities arriving from Italic tribes. When you see at Rome a temple or a reference to Jupiter Dolichenus or to Jupiter Heliopolitanus, or where in the provinces there is reference made to Jupiter Apenninus, those titles distinguish that these deities were considered to be different gods from the Roman Jupiter. In the cities of provinces, at the center of town, would be built a Capitolia, or temple districts dedicated to Jupiter Capitolinus, where again Roman Jupiter was ditinguished from the Jupiters of other nations. Adoption of a foreign deity into the Roman pantheon was signified by having a temple built at Rome within the pomerium. Thus the fight over Isiac shrines being erected inside the pomerium was not over a policy of tolerance towards Isiacism, but of Roman acceptance of Osiris and Isis into the Roman pantheon. The other place where foreign deities are indicated as accepted into the Roman pantheon is where their festivals were included into the Fasti. For example Celtic Epona.
Syncretism involves something different than foreign deities being recognized as gods in their own right, or their being recognized into the Roman pantheon. The Greeks would recognize the deities of other nations as being aspects of their own gods. That is what syncretism entails. Egyptian Thoth was not considered by the Greeks to be a different god, but was regarded to be a local aspect of Hermes. Attributes of foreign gods were then grafted onto Greek gods to emphasize that they were the same gods and not just similar gods. With imperial Rome syncretism did grow in certain intellectual circles. Syncretism was more a philosophical theory than a religious practice. Imperial Roman policy was to respect and maintain the ex patria culti deorum at every locale. Therefore Romans who went to different parts of the empire would participate in local celebrations while still maintaining their own practices in the Religio Romana, and accepted that foreigners servicing in the army or administration, or living at Rome, would maintain their own ex patria culti deorum while participating in the local festivities of wherever they happened to be living.
This policy on the ex patria culti deorum was extended towards Judaism in a unique way. The Greeks and Romans respected Judaism as an ancient tradition and considered their teachers to be philosophers. Philo of Alexandria was viewed and respected as a philosopher and it was only incidental that he was a Jew. Because the Jews were respected as having their own ancient tradition, the Romans allowed them certain exemptions with regard to participation in the ex patria culti deorum of other communities. Judaism was unique in teaching that its practitioners not participate in rites towards foreign gods, and the Romans, for the most part, respected that part of their tradition.
With Christianity a new situation arose. Initially Romans viewed Christianity as another form of the multitude of forms of Judaism that existed at the time, in the first century of the common era. But as Christianity furthered developed and distinguished itself from Judaism, and as local disturbances ensued within Jewish communities over admitting Christians into their synagogues, the Romans came to recognize that Christianity represented a group that opposed the ex patria culti deorum of Palestine. One problem Romans had with Christianity was that it had no ancient tradition, and in most forms of early Christianity there was even a rejection of the Judaic ex patria cultus. Further, some forms of early Christianity, although not all, rejected participation in the ex patria culti deorum, and its members even rejected the divinity of other gods, thus the charge of atheism that was leveled against some Christians. The problem was in certain forms of Christianity and not in Roman policy towards Christianity.
Rome never did come to persecute Christians to the extent later Christians claimed. The "Great Persecution" under Diocletius fell on only twelve Christian leaders, a few being executed but most only having their property confiscated. Other "persecutions" occurred at local levels, in most cases performed by Jews casting Christians out of their communities or by one form of Christian against a different form of Christian, while in other cases it was the local pagan comunities who conducted their own persecutions of Christians. You can recognize in some stories that it is 'orthodox' Christians who persecuted Gnostic Christians, or Gnostic against orthodox, Arrians against non-Arrians, and so on. With the letters between Pliny the Younger and Traianus you can see that agitation for persecuting the Christians came from the local population, not by imperial policy, and Pliny goes so far as to tell Traianus that as the local governor he has greater problems with the Bacchae than with the Christians. Stories of Christians being tossed to the lions at Rome in the Colleseum never took place, as any guide at the Colleseum today will tell you. Tales of Christian martyrs, in many cases being ridiculous fantasies of surviving all sorts of torments first, did not appear until centuries after they supposedly occurred. Early Christian writers conducting debates among themselves and with pagan philosophers make no mention of these supposed martyrdoms. The policy of imperial Rome towards early Christianity was generally one of tolerance, except at local levels when it threatened civil unrest, and was one quite in contrast to the policy of persecution later conducted by Christians against pagans.
Elsewhere there were attempts by Romans to engage in discussion with Christians and attempts to understand their philosophy. Paul, in one of his epistles, refers to his exchange of letters with Seneca. Some letters have come down to us purported to be those of Seneca written to Paul. These are most likely later Christian forgeries but were based on the tradition that Seneca and Paul were in communication. The most widespread form of early Christianity followed after the teachings of Valentinius, who was a student of Theudas, a disciple of Paul. The centers of Valentinian Gnosticism were at Antioch, Alexandria, and Rome, while other forms of early Christianity were more locally limited. All of the churches to which Paul wrote his epistles are known to have adopted Gnosticism. Valentinius himself came to Rome and founded a Christian school there in 139. He turned down an offer to be made bishop of Rome in 143, and died peacefully at Rome in 155 without ever suffering any Roman persecution. Plotinus is known for writing a philosophical treatise against the Gnostics, most specifically against the Valentinians Adelphius and Aquilinus. It has since been wondered why he did not mention other Christians as well. The simple explanation would be that early mainstream Christianity was Gnostic, as can also be seen in the writings of Paul. What emerged later as an orthodox tradition opposed to Gnosticism was most likely a heretical movement inside Christianity. The first attack against Valentinian Gnosticism arrives with Irenaeus of Lyons in 178 after Valentinius' death. Plotinus is later and it seems that this 'orthodox' or 'literalist' form of Christianity had not yet arrived at Rome in his time. With Porphyry, Celsus, and Origin you can see that the real conflict between Christianity and paganism, and within Christianity itself, was conducted not in political persecutions but in philosophical debate. Mention is also made later of Alexander Severus placing an image of Jesus in his private lararium, alongisde that of Apollonius of Tyana. In that case Jesus and Apollonius were both regarded equally as wisemen and as miracle workers. Celsus, writing around 125 CE, compares Apollonius with Jesus as two holy men, healers, and philosophers. [You can find out more about Apollonius of Tyana at
http://www.theosophical.ca/AppolloniusTyana.htm ] In all of this you can see that there were attempts made to tolerate and integrate early Christianity into Roman society and into the imperial intellectual life.
With Severus it can also be seen that the Romans did not have a problem accepting aspects of Christianity into their own practices. On the other side, early Christians had no problem participating in the ex patria culti deorum of their cities. Early Christians were an integral part of imperial society, extending into all classes of Roman society. In answer to your question, I would say that through the second century Christianity was perhaps distinct but not in conflict with paganism. The change comes in Christianity itself. First there are doctrinal disputes. Then there is complaint by some Christians leaders over Christians participating in the ex patria culti deorum. There began a movement in Christianity late in the second century that was exclusionary, that refused to be integrated into the imperial society. This new movement can be compared with today's Christian fundamentalism, as it emphasized a literal interpretation of sacred texts where Gnosticism did not, it emphasized a Christian reinterpretation of the Judaic texts where Marcius had rejected Jewish scriptures as replaced by the teachings of Jesus, it inverted the teachings of Jesus from universal brotherly love into a religion of exclusiveness, and emphasized rigid conformity in practice over individual spiritual growth. The new literalist orthodoxy also rejected participation in Roman society, whether in participating in civil festivities, in the army, or in civil adminstration, and made its main attacks against those Christians who did integrate in imperial society.
So I would say your question is basically misstated. It was not a matter of why Rome could not integrate Christianity alongside the pagan culti deorum, but rather why a certain form of Christianity came to be so intolerant towards all other faiths including other forms of Christianity?
Vale optime
Marcus Moravius Horatius Piscinus