Hot Rod was the chosen one.

Chosen by HASBRO!

...seriously, they needed a damn good reason to plug the Rodimus Prime toy - it's a crap toy (even by 1986 standards)! Ultra Magnus was a much, much more awesome toy for that year (even though it was designed years earlier as part of Diaclone) and intuitively made more sense as the next leader (since he was pretty much the same mould as Optimus Prime, but with a super mode/apex armour!).

Heck, Hot Rod is a better toy than Rodimus Prime.