The writers need to do start introducing the villains much earlier in the saga and actually have them do serious things. They tried that with Team Skull in the Sun and Moon saga by having them appear in the 2nd episode, but then they totally ruined that by making them into the Three Stooges. We need serious villain plots, not comedy crap.
A reminder that Team Magma did appear in the 2nd episode of AG, while Team Aqua appeared later in the 17th episode of AG. In addition, they were doing serious stuff in their debut, such as kidnapping a Professor to enter ancient ruins as well as infiltrating the Devon Corporation.