Not anymore!
Sun and Moon saw the introduction of Team Skull and the Aether Foundation; the latter was ostensibly a force of good before being revealed as the games' main antagonist. Ultra Sun and Ultra Moon also introduced Team Rainbow Rocket as the main focus of the postgame.
In Sword and Shield, Team Yell served as the main baddie and is the only real "evil team" in the region. That said, Macro Cosmos does oppose the player during the climax, though this is mostly thanks to Rose and Oleana rather than the organisation as a whole.
From Red and Blue to Black and White 2, there have been five villainous teams: Rocket, Magma, Aqua, Galactic, Plasma, and Flare. Aqua and Magma are the only ones to appear as primary antagonists side by side. However, in Black and White 2, Team Plasma is split into two opposing factions, so it could be argued there are two villains there as well, but it is really only one of the factions (Ghetsis' faction) that is evil, with the other faction (N's faction), actually helping you along the way.
However, in the side games, teams do appear together. Team Snagem and Cipher were both in Pokemon Colosseum for example. In addition, in XD: Gale of Darkness there are multiple teams, including Cipher and an offshoot of it called Team Miror B., but only the former poses a significant threat. I may have missed some examples.
Hope this helps!
