The Germanic and Norse religions are rather... grim. Christianity is very hopeful and idealistic about afterlife and posthumous rewards, but the pagan faiths are pretty fatalistic or even nihilist at times. Hel exists, but the alternatives are either eternal nothingness or a place of eternal training for a doomsday that will destroy everything (that's only for warriors who die in battle and women who die in childbirth.) Roman polytheism was much the same way, though a little lighter and with a dash of hedonism. I can't comment on the intellectual side of things, though I imagine it wouldn't be as strong.
The Dark Ages may have truly been dark.
At least a few of the Greek mystery religions were moving towards reincarnation, which might have alleviated some of the fatalism. Alternatively, I believe the goddess Isis at the least offered her followers some sort of redemptive afterlife. The idea might well spring up absent Jesus - after all, the clear portrait of the afterlife is very much a Christian innovation on Judaism.
Also, while they're perhaps less resilient than monasteries, I expect that the elite classes and various academies and libraries in the east at the very least would preserve the intellectual traditions of the Greco-Roman world.
As to some of the other comments I've seen, I don't see why "mother goddess" cults have to be too exclusive. What if Isis is an aspect of some sort of platonic divine and also has a husband named Serapis who covers the male elements of divinity, and you can worship them together as the true names of the God? Wouldn't something like that be appropriately universal.
In general, people liked the rituals of paganism - they were tangible and in times of peace provided for a well-regulated, well-ordered world. Where they fell down, I think, was that they didn't provide enough of a community in times of upheaval. The trend in the Roman world is going to be towards universal religion to match the scope of its empire. The various mystery cults will have to adapt a lot to survive.
Unrelated thought - without Arianism to define them against the Chalcedonian Roman world, might the Germans assimilate even faster?