The most memorable video games of my childhood were Final Fantasy 2 (aka FF4 in Japan), and FF7. And the most memorable moments from those games are when they killed off playable characters that I had become quite fond of. Those 16 bit graphics on the SNES, combined with the right musical score, could create a pretty moving experience. I never had a Tamagotchi, but I can understand how the loss of a digital pet could…
I did not notice how dark some themes in the game were until later in life when I replayed the game. Seeing an entire city being poisoned, magical robots built with energy drained from enslaved magical creatures, murder, suicide, poisoining, mind control, abandoned babies, feral kids, cults, fires, cataclysms, possessed artwork, trains to the afterlife, tyranny, etc.
But that's part of what makes it a great game.
The SNES had many good JRPGs in addition to Final Fantasy, like Chrono Trigger, Secret of Mana, Seiken Dendetsu 3 (aka Trials of Mana), Super Mario RPG and others. They are worth playing even today.