Disclaimer: Yes, I am aware that Fiddlestick's current direction is that he's so ancient nobody really knows where he came from. But this is just for fun.
I'm thinking Fiddlesticks was the first attempt to create a weapon out of shadow magic; the prototype for things that would eventually become demons like Nocturne, Evelynn and Tahm Kench.
It's heavily implied in Nocturne's lore that the first demons came about because of shadow magic; specifically, mages harnessed darkness and evil in order to create weapons to use against their enemies, in the same way Zed creates shadow clones to fight with him (but with more will of their own). Shadow magic has been forbidden for millennia (and is implied to have been so even before the Rune Wars) but the fact it needed to be forbidden implies there was a point in time where it was not. The fact that Zed's use of shadow magic has not instantly backfired on him would further suggest that when shadow magic was first discovered, its dangers were unclear (as opposed to, say, a darkin weapon which would instantly sieze control of the body of a weak-willed wielder). So mages would experiment with it, find new ways to harness it.
At some point, someone would try and create a weapon using this magic. This initial prototype would be rough, unfocused. It was a proof-of-concept, not an actual weapon itself. But since shadow magic can form a will of its own (as evidenced by the existence of demons) the prototype would become self-aware, both of its existence and its purpose: to hurt people. Which it couldn't do so long as it was contained by its human masters. So it strained against the bonds, breaking them open and pushing out. You can see in its recent update that when Fiddles gets excited, it pushes its shadowy limbs out of the cage in the center of fiddle's chest and uses them to help it run faster.
Fiddles would not particularly care what it looked like, so long as it could kill and hurt people. So it grabbed what it could and leashed the bits to its will. Unlike Evelynn or Tahm, it had no real need or desire to lure others in, and so never developed any kind of human form or intelligence. (It didn't even need to out think its prey like Nocturne did or prolong the hunt, so it didn't need to develop intellect). It simply charged out and killed things, as it was meant to do. It's an ambush predator.
It's not a perfect theory by any means, it doesn't really explain why Fiddle would be a scarecrow in particular, but I like it.