Since he was written for the Holiday Special's animated part, Fett was possibly not originally Lucas' character. Someone likes him enough to use him as a plot device (-Be it Lucas? Kasdan, or Brackett more likely), and Lucas is genuinely surprised at how beloved the character becomes. Maybe he feels like Fett somehow overshadows his own characters-so much so that he feels like he can't NOT put him in Jedi, but resents the character to the point that he chooses to off him as comic relief. (Seriously, even as a child, who wasn't perplexed at how weak he was killed in Jedi?)
Years pass, the prequel ideas are percolating, and he's accepted that people love Fett as a badguy regardless, and he figures "Okay, let me use Fett to make the Stormtroopers cooler!" and poof, all the clones are Boba Fetts of one slice or another. He does the one thing that cuts down the joy of the Mandalorian- He makes him commonplace.