Rumpelstiltskin and Cora
I think the Rumple and Cora twist was interesting, and there was a lot of history there between the two characters and even Regina years later. But it was still kind of a weird relationship to see. When the two get closer, you want to cover your eyes! At the end, we see how selfish the both are, thinking about power. Especially Cora. I don't know if she ever really cared about the Dark One, or he was just an means to an end. Either way, it made for a bad relationship.
Emma and Neal
The show likes to try and make us forget the biggest issue when it comes to Emma and Neal's relationship - Emma was underage and Neal was quite a few years older than her. This definitely makes this relationship wrong in any book. Neal was also selfish. If he really loved Emma, he could have found a way to still be with her while helping her fulfill her destiny of breaking the curse. Instead, he was more afraid of his father, Rumple, finding him. So he chose to run away and leave her alone. Henry came out of this relationship, but it definitely wasn't a healthy one.
Zelena and Hades
I guess there wasn't anything necessarily wrong with the Zelena and Hades pairing. Both of them at the time are evil characters, and they weren't going to change that. That's just what it was. I think they're more on the "worst" ranking for me in terms of I wasn't really invested in their relationship. It wasn't really an interesting storyline. I think lots of you fellow fans would agree. Just in terms of a villain, Hades was kind of boring too. But that's a different story.