Dont think so, it also means pokemon with moves meant to super effect their coutners (things like Blissey with DG and ZH against machamp) or pokemon that naturally are weak to the pokemon they coutner (like gengar) take more damage. Metagross still stands tall as a great blissey coutner because the aforementioned machamp taking (as well as dealing more damage agaisnt blissey) more damage from those moves while metagross resists them harder. Rayquaza probably did take a hit, Mewtwo still is great because of great stats, though on release, Darkrai will be a much better anti-ghost/psychic specialist, though mewtwo is the superior generalist.
Generalists likely arent completely gone, but their utility has diminished. Generalists never were the best of what they fought against, they were great because they were useful in a lot of situations while specialists were either very expensive or limited usage, and that same thing still applies. Something like powering up a single pokemon for 80% of offense and being in the top 10 or one pokemon for say 5% of offense, but being top 1-3.
TL'DR, generalists arent over with, what made them great still makes them great, but it does put specialists above them more so
For PvP, it makes counter coverage more threatening