The bigger difference between the two was that Transformers: The Movie mattered in its universe -- a lot -- and G.I. Joe: The Movie didn't. In fact, G.I. Joe: The Movie, IIRC, was the end of the cartoon series and never built on the new characters it introduced.
With Transformers, the new characters introduced in the movie were thrust to the forefront precisely because the old characters were killed off. They take on a huge role because they're among the few survivors of the Battle of Autobot City, not necessarily because the older characters have just disappeared. If it glosses over their introduction and individual back stories it's because they're fighting and then running for their lives the entire movie. The new characters also mix in with some of the older ones. Bumblebee, the Dinobots and a few others all survive the movie and are featured throughout it.
The G.I. Joe movie was a lot more ham-fisted with the introductions, and the existing characters barely show up at all even if it was just to be killed off or phased out.
Also, since there was another season of the cartoon, they were able to build on the movie's long-lasting consequences.
You had Unicron's head still orbiting around Cybertron and posing a threat; Rodimus Prime trying to be the guy who follows The Guy as the leader of the Autobots and struggling to live up to the task; the Decepticons in shambles after losing the war; and plenty of other fallout.
They did bring back Optimus Prime (and Starscream) during the next season of the cartoon, but the other Transformers stayed dead or altered.
The episode where they brought Optimus back was kind of creepy. The Autobots come across a mausoleum in deep space that contains the bodies of those who died during the movie, which are eventually destroyed forever. They find Optimus as a mind-altered zombie that, in a great bit of continuity, still has the same battle damage from his fight with Megatron, and he rides to his apparent (but not really) second death in a shot where he's on fire with one arm and one eye missing.
The final season of the cartoon felt a lot more "grown up" and darker than the first two years of shows.
Long story short, the Transformers was able to take what has largely been defined as a cold-hearted cash grab and turned it into the defining point of its narrative saga. If you chart the four-year story arc of the Generation One Transformers, it's almost like a trilogy where there's the stuff before the movie, the movie itself, and then everything after. And almost every other iteration of the Transformers since has worked pieces of the 1986 movie -- like Unicron, the death of Optimus, and the Megatron/Galvatron transformation -- into its story as well. Calling it just a way to kill off one set of characters and introduce another really doesn't do justice to what they ultimately did with it.