I know that many polytheistic religions believe in some higher power above the gods, which is either the actual controller of everything or which actually is everything. For Ancient Greece, the power was the Fates. From what I've read of Ancient Greek literature, they come up a lot, but never really as characters in their own right, rather as a vague, mysterious force the characters have to work around. Is this universal, or are there pagan stories where the ultimate powers beyond the gods are portrayed as characters with recognizable personalities, emotions, and motivations in the same way that, e. g., the Olympians in Homer's epics are?
I can only speak for Ancient Greek myth but I'm sure others will be able to share about other pagan mythologies!
It's funny you should mention Homer because the fates begin to emerge almost as characters in his work, we get a rough sense of their existence for example in Book 16 Zeus knows his son must die due to this fate and when Hector faces Achilles, Zeus seems to be the arbiter of fate weighing up both their souls with a predetermined outcome. Though as individual characters they are more alluded to here and in their role more as a force than anything.
The fates in Greek mythology do later get personified, they are known as the Moirai and, according to Hesiod, were the children of Erebus and Nyx, both associated with darkness and night. It is from this that we get the image of the weavers of fate - one sister to spin the thread (Klotho), one to measure it (Lakhesis) and one to cut it (Atropos). They very rarely appear in myths and when they do it is often not in a personable or recognisable way. However, in the Gigantonomy they aided Zeus clubbing to death two giants Agrius and Thoon (this is depicted really well on the Pergamon Altar). There's even a story of the fates being tricked where Apollo got them drunk in order to save the life of his friend Admetus, though the Fates did get there revenge in the end instead taking the life of Alcestis, Admetus' wife.
Typically the depictions of them as more 'human' figures come later whereas in Homer they are seemingly more depicted as a force.
Another interesting aspect are the furies (Erinyes). They are sent to torture mortals for crimes and their nature seems to mirror that of the fates across time. In the Iliad they seem to be more of a force, such as in acting against Agamemnon who stole Achilles prize. Yet in Greek drama they take on a life of their own and act as characters even going so far as to take part in the first ever law court acting as the prosecution (according to Athenian playwrights who were ever so proud of their democracy) over whether they should be allowed to torment Orestes or not at the end of the Oresteia.
To the Greeks mythology and religion often intertwined and thus they saw no problem in believing that the fates were a mysterious force that bound the universe together while also believing that they got so drunk they were tricked by a God. An important point in how they are portrayed is the medium - in later art and literature (most specifically drama) they begin to be characterised yet earlier works they are not. The reasoning behind this perhaps has something to do with the transition from the so called 'dark age' of Greece into the more famous country of plays, art and philosophy in classical Athens, as the Greek way of life changed so did their portrayal of their Gods. This last bit is just my own opinion though and most definitely up to interpretation!
Hope this helps!