Ultra Magnus has a very memorable moment in the episode "The Two Faces of Ultra Magnus". When Megatron starts stomping on the Autobot brothers, concern for them causes Ultra Magnus to receive an exponential power-boost. The energy is then transferred into the three Autobots, who then use there new strength to blow Megatron away. While it's a small moment, it's the first of many that proves Ultra Magnus isn't all that bad a guy.
Optimus: Magnus, you came to earth for the Matrix. But you don't understand the responsibility that comes with it. It's my duty to stop Galvatron and protect the earth!
Ultra Magnus: Oh I understand alright.
Optimus: Then why did you remove me from the battlefield? We have to go back and fight!
Ultra Magnus: Right now pal your in no shape to fight anybody.
Optimus: You're right. And that's why I'm asking for your help this one last time.
Ultra Magnus: Wait a minute, are you sure your really Optimus Prime? Cause that sounded like a request, not an order.
Optimus: Magnus, I never wanted to control you. I wanted you to join the Autobots because of your value as a member of our team. Maybe we'll resolve our differences. But right now the only thing that matters is stopping Galvatron. Will you help me?
Ultra Magnus: ...One last time, we'll stop Galvatron together.
Optimus: Thank you Magnus.
By the end of the series, Sky-Byte not only escapes capture. He's apparently reformed too.