Okay, but Ultra Magnus was a big ticket item for Hasbro to push in 1986, so it made sense for writers to make him cool to try to elicit more kids to buy him. Also, being such a big toy, it kinda made sense that he would be powerful (though nothing wrong with small toys being strong - that's something I liked about Brawn

). Also, they were preparing to have Ultra Magnus become an arch-nemesis for Galvatron -- and Galvatron is insanely powerful in the comics... so while Magnus did repeatedly get nine colours of snot beaten out of him by Galvatron, just the fact that he was even able to go up against Galvatron meant that he had to be pretty powerful.
To me, it felt intuitive for Ultra Magnus to be the powerful Autobot leader in Optimus Prime's absence. He seemed a worthy heir... a lot more worthy than the incredibly underwhelmingly disappointing Rodimus Prime. And regardless of what you think about Ultra Magnus, he didn't get
that much canonical exposure, thanks to the fact that:
1) Rodimus Prime was the real "flagship" Autobot hero and thus was 'prioritised' over Ultra Magnus; especially in the cartoon
2) In the G1 comics Ultra Magnus only existed in the "future" and not in the "mainstream" universe of the 'present day'.
Who else would you rather see promoted as the Autobot hero from the 1986 line? Would you prefer Rodimus Prime over Ultra Magnus or someone else entirely?