This may be from my generation which probably precedes by about 5-7 years, but I was exposed to the Japanese exports such as Battlestar Galactica and Robotech, which I loved, despite the sci-fi genre, were "realistic" where war and conflict resulted in deaths. Deaths of major characters! Robotech probably produced, through the Transformer toyline, the best toy, Skyfire/Jetfire, which was based off the Robotech Veritech YF-1J.
Also, there were some dark tones with shows like Galaxy Rangers, Orbots, etc.
With respect to G.I.Joe, they did finally kill off a main character, Duke. Also, there's the transformation of Cobra Commander to a well... giant cobra. In Transformers The Movie: TONS of deaths. Ironhide, Prowl, ...everyone on the shuttle coming to Earth, eventually to Optimus Prime.. and that was just the "good guys".
Last but not least, touching on the "PSA" portions of cartoons, look up G.I.Joe PSAs on youtube. I imagine they will entertain greatly.
P.S. noteable mentions: Jayce and the Wheeled Warriors, Bionic 6, Gummy Bears (the whole disney onslaught of the early 90s, Ducktales, Chip n Dale, Gizmo Duck, etc.), Freakazoid, X-Men and Spiderman, Batman of the early 90s with that style of futuristic art-deco, anyway.. i could go on.. but thats my $.02.