I remember that episode! That was so heartbreaking. His HeartGold Wedlock series is probably my favorite series.The one Jolteon I do hate is the one from the Kimono Girls in Marriland's Heart Gold Wedlocke. It killed his Feraligatr, Gengar and Tauros, but did get avenged by Tauros' partner, a Jumpluff. Sadly she fell to Vaporeon's 4x super effective Aurora Beam.
I like that the anime portrays things that way. I don't know if the manga does the same. But is there really any way for the games to portray that without losing their "catch them all for a reward!" deal?When you think of it, it's kind of odd legendary Pokémon are even capturable, locking away a god in a tiny sphere. You'd expect the environment to get completely out of control if you for example catch Rayquaza and Kyogre, but leave Groudon around.