Pokemon will always be a children's game, so death will never makes its way into the pokemon games. If you want an element of death in pokemon games, you could always try a nuzlocke run.
Did you forget about the Pokemon mangas? They have Pokemon deaths in those.
I remember where Gastly ressurected zombie Pokemon in the Pokemon Tower in Lavender town. and Red kept sweeping through those zombies. And at one point, Koga sent out his Arbok against Blue's Charmeleon, and Charmeleon used slash to cut Arbok in half.