The problem isn't that there's 12 Pokémon per episode, it's that you'd only ever see the peripheral Pokémon once every 12 episodes, at best. But I agree with the rest of your sentiment.
Not really, think if It this way...
TR gets promoted by Giovanni (and the writers basically) to try and capitalize on controlling the Alolan islands and that starts first with building a team and use the Z-Moves on their Pokémon, then beating Team Skull, challenging the institute, etc.
Assuming Jessie and James can use rideable Pokémon as they get paid from their new positions: Jessie can use Charizard to investigate from the sky, James can use Lapras to transport the team to different islands, Taurus and others can be used for land transportation. (The benefits of the region is that rideable Pokémon are rented and don't need to be caught).
Jessie and James focus on trying to catch Pokémon to capture the Tapus, so they aim for Steel or Poison types and just use them with the Z-move crystals they find.
If you make the Trainers important, the Pokémon become important by default, as long as they are featured in the missions. Maybe because the legendaries are strong they have to use multiple Pokémon to beat them. They capture a few, use their strength to make up for being outnumbered by Team Skull, win, the institute defeats Team Rocket and takes the tapus, before ash steps in to defeats the institute, when ash is preoccupied by facing the institute, they take control of the ultra beasts and are now who ash has to face, and suddenly, TR matters again...
See? And just having some Pokémon is used to explain how they win against the fact they are out numbered.
If butterfree can get a close bond due just to a few episodes after it was caught (he even traded it away for a Raticate... randomly), and it didn't appear in every episode since it was caught, then I think it is safe to say that many Pokémon that are established as important will have enough of a plot line to be relevant and not pointless.
(People actually remember Butterfree more than Pidgeot, in spite of the facts that Ash used Pidgeotto throughout his entire Kanto journey, it was caught in the same episode as Caterpie, and it had a great goodbye episode which basically capstones the entire first generation in relation to the very first episode). All you need is a few good bonding moments and people care more about that than overall episode exposure spreadout during the seasons.
Remember whenever Ash's dragon Pokémon from Kalos was rumored to return for the League to complete his team of 6?
Clearly, less of exposure than anything else, but people were more excited about the fact it hadn't lost up until that point than his bond with Talonflame, Noivern, etc. because that established an important role!
If a Pokémon continues to be undefeated, then that must mean he will win if he uses it... therefore role trumps episode storyline exposure.
(They thought based on that Ash would win the league and make the show special).