The latest issue of the Star Wars Insider magazine tells us more about the Fett connection in the prequels. Here's their quote from George Lucas:
"He is a background character, but I needed a device, a bounty hunter to do things. That particular bounty hunter had become a rather popular character, and even though people were writing all kinds of things about where he came from, in my mind he was always connected to the stormtroopers. I realized I could use Jango Fett as the bounty hunter, and he would be Boba's father, and then it all fell into place. But even if he wasn't a popular character, it probably would have fallen into place. There are lots of little stories going on in [EPISODE II], sidebars of how things came to be. Some of it was written back then, mainly the main characters. But all the secondary characters, like Boba Fett, were added later."