I'll be honest, I really don't like the Vishnans. I don't feel ascended energy beings like them belong in the FS universe. Even the nemesis of every subspace-using species, the Shivans, are flesh and blood.
Or to sum up everything: I think BP's mysticism does not fit at all with FS. We have two games and an expansion, and
never added any mysticism. Mysteries, yes, but they never went off the deep end and claimed Terrans and Vasudans were receiving psychic messages from unknown all-powerful psychic beings. I find the Shivans being one race of three that existed to create and preserve life takes away a lot from the aura of pure evil they had in FS canon. I wonder if BP3 is going to turn out like B5's Shadow War with the Vishnans and Shivans killing each other over whether or not humanity gets to stay alive with the Terrans and Vasudans trapped in the middle of these dueling ancients.
EDIT: Let me clarify. I think BP tells a great, riveting story. I simply don't think it meshes with the existing FS background very well.
On the contrary, I believe that the Shivans have been alluded to as metaphysical janitors since the cutscenes of Freespace 1. Freespace has long been steeped in Hindu mythology. Even the word "Vasuda" is the sanskrit word for Earth. The slaying of Ravana via Helios (Sun god) bombs is a particularly tongue-in-cheek reference, as avatar Rama performed a prayer to the Sun god Aditya in order to gain the strength required to shoot his arrow through the chest of Ravana, killing him.
Perhaps this is just because I enjoyed Xenosaga so much that I have this view, but I think it makes perfect sense within the realm of science-fiction that a metaphysical entity from a higher realm would need some sort of avatar/body/ship to use as a proxy for interaction with the lower realm; a vessel to carry out its will, or an entire race of vessels. Angels and avatars. Xenosaga changed up the formula a bit by proposing that "God needs a starship" rather than a race, and Blue Planet combines both ideas in the Vishnans and Shivans. The Shivans are more material, with actual bodies building their ships, while the Vishnans are pure consciousnesses inhabiting the ships. You could say the Shivans are the lower, more material manifestations of metaphysic beings while the Vishnans are higher.
The Shivans are a collective. They are literally a single organism/being with many separate parts, like a jellyfish or ant colony. The totality of Shiva's collective consciousness could qualify for demi-god in size and willpower.
Shiva is the destroyer deity of the Freespace universe, planned for this role by Intelligent Design, and perhaps even birthed from the flux of Subspace itself. Shiva destroys failed races which have not overcome destructive tendencies to pave the way for future races, much like the God of the Old Testament destroying the world in a flood to give the righteous Noah a chance to reboot humanity. Likewise, Vishnu the Great Preserver and its parts (the Vishnans) destroys to preserve races which already exist.
Shiva and Vishnu are two aspects or faces of the same being in the trinity of Brahmanism, and so their roles are highly similar. Together they restore and uphold balance in all things. In fact, it could be said that it would have been more proper for the Shivans and Vishnans to be a single race, because they literally "destroy to preserve." The only real plot hole in the metaphysics of Blue Planet is that, before the Shivans began to destroy indiscriminately and forgot their sacred purpose (much like the assessor Satan in Christian theos), there was no real reason for a separate race of Vishnans to exist. The Shivans would have simultaneously been Vishnans in action by preserving budding races like Terrans from destruction at the hands of the Ancients.
I quite like having metaphysics in science fiction. After all, "any sufficiently advanced technology is indistinguishable from magic," and any sufficiently advanced entity is indistinguishable from an angel or god. Xenosaga did wonders with Gnostic metaphysics and the new Battlestar Galactica had comparable success with its angels and creator deity that doesn't like to be called "God". I think Blue Planet is right at home among them as one of the better, more ambitious science-fiction tales to date.
Frankly, I think after the Matrix shook things up, any science fiction tale of large scale and hoping to raise the bar of ambitious scope is lacking without at least some metaphysical or mythological reference. The Blue Planet team should get HUEG props for being brave enough to continue the budding tradition.