Binder pages by @pokejade_ and @imbabypoke By TCG Era or Pokmon Generation Organizing by Pokmon generation or TCG era: Gen 1 Pokmon together, Sword & Shield era together, vintage cards together, and so on, is a good middle ground between organizing by set and organizing by Pokmon
If youre running a token deck, you can probably spare 7 creatures to give the other 9000+ a free Overrun
in the previous set, Ursulas Return
Find Esper Sentinel or Skullclamp fuel
In addition to retailers, you can join Pokmon TCG communities in-person or online, like the Danireon discord, which may allow you to trade cards with fellow collectors
With the rate at which Magic: The Gathering releases new Commander precons, there's bound to be some overlap in deck themes, reprints, and new design space