The main evidence (if that´s the word for it) against Christianity is the delay of the Parousia. The apostles expected the apocalyptic return of Jesus during their lifetimes. When this failed to happen, the second advent was postponed. First a little while, then longer and longer into the future. Early Christianity was a failed apocalyptic sect. Like many others. But you knew that already.
The second best evidence is that there was *another* failed apocalyptic sect which emerged about a century before Jesus. Yes, that would be the Essenes. The fascinating thing about them is that they interpreted what we call the Old Testament in an "esoteric" way strikingly similar to early Christianity. The OT was really about them and their sect during the end times. They believed in a "New Covenant". Their leader, the Teacher of Righteousness, was persecuted and perhaps even killed by the Wicked Priest in Jerusalem. They believed in two Messiah figures: a priestly one and a royal one. Jesus combined both in the same person. Like the Christians, the Essenes applied Psalm 22 and Isaiah 53 to their leader. The Teacher was the suffering servant who would (soon) be vindicated by God.
The Essenes also rewrote the Jewish Law without abolishing it (compare the Gospel of Matthew) and believed that the Teacher had the right to reinterpret the Law due to prophetic inspiration (compare the Sermon on the Mount). There is a strong dualist tendency: the Sons of Light will fight the Sons of Darkness in the final war with evil. Again, compare early Christianity. The 144,000 in the Book of Revelation are probably intended to be celibate warriors. Like Qumranite millennarian monks? Note also that both Essenes and early Christians used the First Book of Enoch.
Of course, there were differences, too. In the NT, the Essene-like John the Baptist recognizes the supremacy of Jesus (who is described as a more complex character). Paul de-Judaizes early Christianity, although he faces opposition from James, said to be the Brother of the Lord. And while Christians rejected the Temple de facto (like the Essenes), it´s strongly suggested that they continued worshipping in it until AD 70. Essenes were for armed struggle against Rome, while Christians opposed it and instead awaited a purely supernatural intervention. The most dramatic difference is the resurrection narrative: the followers of Jesus believed that their master *had already* been vindicated by God. Further vindication would follow in the near future.
That vindication never came. But Christianity managed to transcend the Essenes anyway and became a Gentile-dominated world religion. They shed the skin of Judaism altogether. Well, almost! Christianity has been plagued by constant resurgences of apocalypticism and Judaizing. Indeed, the main inspiration for the former is the strongly Judaizing Book of Revelation. It´s as if the shadow of first century Jewish millennialism is still haunting Christianity...
And that seems to be the best evidence against it.