1. Different mythologies don't always play nicely together. What are the gods, for example? Are they hugely powerful? Are they immortal? Some cultures have very similar understanding of gods or magical beings. Some don't. Sometimes these differences make for interesting stories, but other times--or more to the point, other ways of handling them--can just make one culture look like the Little League in syncretist baseball. Which leads me to:
2. Playing with this stuff isn't always respectful. You are not, of course, required to care. (Readers, in turn, are not required to not get really mad at you when you don't, if they see fit.) But when you do care, having their belief system put alongside something a twee 19th century white person made up about fairies as equivalent may genuinely upset readers in ways you were not hoping for. Go ahead and skewer whatever religious/philosophical powers that be, but deliberately, thinking about it first.
3. You get distortions from false equivalencies. I know this one from some of my own favorites, because how many times have I shouted at a book, "People, Loki is not Satan!" or, "Gahhhh, Odin is so not Zeus and neither is Thor gahhhhhhhh!"? Too many times, I tell you what. It's all very well to spot universal or near-universal human needs, but humans have found extremely different ways to express their relationship with those. Having every sky god come out Jupiter--or insisting that everybody has a powerful sky god really, so that's who this obscure spirit has to be--can make your work shallow and annoying instead of rich and diverse.