Alright, let's put aside what it MIGHT be.
What's the funnest/most interesting theory for what it is? Even if said theory is debunked by now.
I've always found the theory that it was an Aztec manuscript pretty fun. Basically, the Aztec had stupid advanced bonotanical science for the time period, having tons of botanical gardens for emulating specific biomes across mexico, studying their medicinal properties, breeding thjem, and categorizing them "scientifically" in a almost proto-taxonomic system, We have some surviving Aztec bonotanical encyclopedias, such as the Badianus Manuscript.
So some researchers thought that it had a similar origin, and perhaps the unknown language in the Voynich might be some early attempt to trancribe Nahuatl, the Aztec language, into it's own syntax rather then just translating it into Spanish as other surviving/colional era aztec documents had been.
http://cms.herbalgram.org/herbalgram/issue100/hg100-feat-voynich.html?ts=1563930398&signature=ef7fbdedd2f9752498a5fb28b656bf43 is an overview of their research.
However, most Nahuatl linguists think the theory is bunk:
http://nahuatlstudies.blogspot.com/2018/12/was-voynich-manuscript-written-in.html 
