First off, I've labeled JMS an idiot after what he did to Wonder Woman so he's no saint. And while I'm at it, I collected the Babylon 5 Micro Machine sets. They were awesome.
While I would agree that the Indiana Jones merchandise wasn't good, you cannot say the same thing about the lego sets. Those were awesome.
And if you want the worst of the worst, look at the Star Trek (2009) toy line. All they did was copy and past everything but the head and put that in a package. The height was the same, the shape was the same and since we're dealing with a crew of all males, Uhura, Spock and Nero were the only ones that stood out. And the toys weren't fun either.
For movies that didn't get the right merchandise that deserve to? That's easy. ALIENS. I know kenner/hasbro did something with the line, but those were taking way too many creative liberties. Of all the characters, the one who never uses a weapon gets the mini-gun? Ha.