Why has Thunudrus-Incarnate usage taken such a massive hit? Is the Dark-type immunity to Prankster really that game breaking for it? Or is Tapu Koko that much better?
Tapu Koko outclasses it as an offensive force in most cases because of the drastically better Speed tier. It can also overwrite terrains in terrain centric metagames, unlike Thundurus.
Bulky support builds have taken a massive hit because Prankster Thunder Wave used to be an incredible insurance move that provided massive utility for teams, but that got nerfed hard with the Accuracy reduction and the paralysis nerf.
Prankster Swagger/confusion also lost most of its value, which allowed Thundurus-I to fish for hax wins when everything else was lost. (Obviously talking about cartridge metagames here.)
The general nerfs to priority moves, like Psychic Terrain and buffed Dark-types, are just the icing on the cake.
Tapu Koko's popularity also makes Thundurus' life harder by the simple fact that teams need to be prepared for Electric-types in this day and age, otherwise they will just get styled on by terrain boosted Volt Switches forever and ever...
Talonflame is also dead, which was one of the main things you'd use a bulky Thundurus-I against.