GI Joe also was going to kill one main character (well, I assume Cobra Commander being written out was also intended as permanent at the time), not a third of the original cast.
If Optimus Prime was the only Autobot who died in TFTM, his death might not be seen as "failing to see that kids cared about him as a character".
Popular, prominent characters like Ironhide and Brawn dying with such little focus, and Wheeljack appearing only as already-dead, is what makes it clear that the reason for the deaths (including Optimus's) was so cynical.
Knowing that the script and storyboards had even more deaths doesn't help either.