>>14197178It doesn't skip them, it skims through them. The only ones that tie into the story they're telling are Brock and Giovanni so we see them in full.
Remember this isn't just a retelling of Kanto, it's made for the following reasons
>provide backstory for newer fans>provide nostalgia for older fans>promote Pokémon X & Y to both of the aboveNeither audience need to see every Gym in full and doing so with take time away from other events not present in other games.