1. I don't see any reason to include items listed on the original, since some of them came true, and others have not.
2.Similarly, I don't see any point of rewriting scrapped mechanics, since they will inevitably return when the opportunity is present.
So, let's begin. Unlike the original, we will start with the ideas used in alternate canons to see if they fit.
Most of the TCG classifications have found in-game mechanics corresponding them.
Dark Pokémon had Shadow Pokémon and Dark-type.
Light Pokémon has Fairy-type.
Owner's Pokémon had N's Pokémon and in-game trades with NPCs.
-ex variants had Mega Evolution, with LV. X being effectively the equivalent of Level 100.
Delta Species have regional variants.
The only possible exception is Crystal Pokémon, but that's a one-off thing, and BREAK Evolution, which is really poor man's Mega Evolution.
While existing ideas can be used for future gimmicks, they really can't be the "next best thing".
A lot of the inaccuracies in the animé has found its way into games one way or the other, but most major element, the "heart of the cards" gimmick, has been installed into the in-game with both Happiness stat and Pokémon Amie.
Several variant Pokémon featured in the Animé can appear in some way or other in the future, but the two main ideas of the animé are:
1. Tournament Battle prior to Elite Four, rather than Victory Road. This idea is used in Pokémon Uranium.
2. More moves than 4, but only 4 being used per battle. Multiple moves are used in Super Eevee Version, which changed game mechanics to fit more in FF games, but this is a bit more different than that.
None of these are major innovations, with the first being end-game, and second being only relevant in late-game and in competitive battling.
Biggest idea in Adventures and other manga is the trainers with special powers. While this can be a cool gimmick for a single game, for the overall idea behind Pokémon as a kid's adventure, this would be borderline heretical.
We see that most of these ideas are really not that powerful enough to create something new. So, where can we go? Well....
Synergy from Pokkén: Serving as a glorified combination of a Z-Stone and Mega Evolution, this idea has some potential, but is effectively already used.
Triple Typed Species: This idea technically exists with Trick-or-Treat and Forest's Curse. This idea can work in two manners:
1. A regular gameplay feature, in which case, most triple types species would be retcons and new species.
2. Additional types, like Forest's Curse, which is caused by either abilities, moves or items.
The latter can work in a gameplay feature of "Type Ores", where the player character gives a species an ore of its type, which grants it a new type and a new move of that type, similar to Rotom forms.
Double Ability Species: This idea exists in Mystery Dungeon, but it is a bit tricky in main games, especially with single Hidden Abilities. Double Ability species can exist in two manners:
1. A regular gameplay feature retconned in, where species that had separate abilities now have both of them at the same time.
2. A regular gameplay feature added in, where dual ability species exist alongside single ones, giving three combinations with the hidden ability.
3. Additional abilities can be caused by moves or items.
In the latter, Smogon's enchanted items idea can work, where items give a secondary ability as long as they are hold, but cannot be removed as they are form changers.
The problem with all three is that there would be no logical or conventional endpoint to them. They can go on forever in theory.