I've seen it argued pretty convincingly that it was actually Julian the Apostate who was responsible for souring Christian-pagan relations. Which makes sense when you look at it from a Christian perspective: there they are, everything seems to be going swimmingly, even the Emperors are now Christian, and then bam! the first pagan to get the throne since Diocletian immediately starts bringing back the persecuting times. Clearly those pagans aren't to be trusted, the moment they get power they'll use it against the Church, better make sure they never get power again, etc.
It certainly played a clear role that Julian acted as he did. On the other hand, his actions were considerably less... extreme, than anything Diocletian did. There was
this thread on Julian recently, where we discussed his policies and ideas. This was my comment on that subject:
A very good book that sets out Julian's character and his religous ideas and goals is Rowland B. E. Smith's Julian's Gods: Religion and Philosophy in the Thought and Action of Julian the Apostate. -- [snip] -- Julian was not planning to exterminate Christianity, or to fully end religious tolerance. (At least: he wouldn't ban Christianity until he had crucially weakened it and meanwhile consolidated his own religion. Smith argues that Julian obviously hated cChristianity a lot, and would probably have banned it for good at a later stage. Do note that this is Smith's reading of Julian's character, and based on conjecture.)
Certainly, heterodox (and localised) versions of the Roman-Hellenic religion would be tolerated. But the new orthodox version of the Religio Romana would enjoy the favour of the state. Christianity would be tolerated, but hindered/discouraged. For instance, Christians would no longer be allowed to open schools (ensuring that education would fall to the religious schools of the Religio Romana, which the state would fund). Similarly, Christian churches had been tasked with the distribution of alms to the poor. Julian planned to make that the task (and the exclusive right) of his orthodox pagan priesthood and their temples, which would draw the poor to his religion. Finally, there would be a specific tax levied on all Christian churches, to repay the damage that Christians had in the past inflicted on pagans, pagan temples etc.
All this would serve to encourage people to join Julian's religion, while make Christianity rather unattractive. The book I mentioned does a far better job laying out Julian's plans, as well as his ideas and beliefs. But what I've outlined above should really be enough to demonstrate that Julian wasn't stupid enough to ban Christianity outright, but that his plans were actually quite realistic and pragmatic.
...so I'm pretty confident that we can't really equate what Julian did (or tried to do) to the mass-murdering frenzy of Diocletian. Of course, perception is subjective, so to contemporay Christians, Julian may have seemed the Great Evil. (His monniker 'the Apostate' certainly implies that they thought ill of him. It's not like Diocletian is styled "the Persecuter" or something.)
However, in a broader context, I think that Diocletian still led to a divide and a mutual hostility, of which Julian was in truth a latter-day outgrowth (on the pagan side of things).
That being said, though, the degree to which there actually was pagan-Christian enmity can also be (and usually is) exaggerated. Julian's anti-Christian laws were almost entirely the result of his own hang-ups, and most pagans thought he was quixotic and slightly ridiculous. Even under staunchly pro-orthodoxy Emperors like Theodosius, who was the one who forbade pagan sacrifices and made Catholicism the state religion, there were high-ranking pagans in the Imperial court, who apparently didn't suffer any disadvantages due to their religion. And, contrary to the claims of "destruction of pagan history and legacy", most Christians in the Empire were eager to preserve their glorious Roman heritage. Virtually every pagan work of literature which survived to the present did so because of all those monks making copies of them.
Needless to say, I fully agree that it's all far from black and white. It's not like all Christians hated all pagans and vice versa. But I do believe that - in no small part due to the way Diocletian had acted - there
was a real hostility that cannot be dismissed. Similarly, I'm certainly not claiming that "the evil Christians destroyed muh pagan learning" (as the historically unfounded 'terrible Christian dark ages'-meme goes). In fact, I will argue to the hilt that Christian monestary culture saved the bulk of classical knowledge in the West after the Western Empire's collapse and the destructive Gothic War of 535–554. My point is more that there was a particular... eagerness to get rid of pagan institutions and works in the earliest two centuries of Christian dominance in Rome, which cooled off afterwards. I link this to an urge for vengeance against the persecutors of Christians, and I blame Diocletian for the worst of
that. (My comment in the other thread, quoted above, mentions the damage that Christians had in the past inflicted on pagans, pagan temples etc. --
before Julian got to power. The book I reference goes into detail. Clearly, there
was early Christian destruction of pagan institutes, to a certain extent.)
I will admit: perhaps I am biased without realising it. It's clear that I dislike Diocletian for other reasons as well, while I have an intellectual admiration for Julian regardless of his faults. So it's possible that even though I try to look at them objectively, I subconciously treat them uneqally.