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Get rid of the leveling system.
>No more level curves
>No more grinding
>No more overleveled play-throughs
>No more EXP Share
You can still raise your stats through other methods like Pokethalon, Super Training, and Gym Training.
Gym Training: You partake in training at any of the Pokemon Gyms. The harder the gym, the more stat points you can earn.
No levels means more world to explore. You aren't restricted or limited to any level cap. A Poliwag can stand toe-to-toe with a Squirtle. A Pikachu is probably going to lose to a Magnezone. This make the gameplay more focused are Type-Matchups and Pokemon Movesets/Abilities. Even though your Pidgeotto is a first stage evolution, if your opponent sends out a Roggenrola, you might want to switch out (unless you actually trained its stats).
Side Quests. Make NPCs actually important. They give you incentives to fill out your PokeDex. Rewards are given to completed quests. They could be anything really:
>Fish a large Magikarp for $500
>Put a Zubat to sleep and catch it for 3 Dusk Balls
>Catch at least 100 Pokemon. Here's a Bike!
Just stop giving us free shit.
Bigger World. Now that we don't have levels, we can have as many regions as we want. Stronger Pokemon are going to be more difficult to obtain. Bigger World means more Pokemon to catch, less Pokemon to trade. Obviously there are going to be version exclusives, but make 80% of Pokemon catchable on one game, 10% through Legenday Events (in game), and 10% version exclusive.
Different ways to catch Pokemon:
Surfing, Diving, Fishing, Grass, Tall Grass, Caves, Mountains, Night time exclusives, Safari, Quests, Honey Trees, Headbutt Trees, Rock Smashing, Fossil Hunting. Swarm Routes. More variety.
Make money harder to get. I'm tired of always having millions of dollars with nothing to spend it on. Clothes are good money burners, but introduce more things to buy, or actually make money more tedious to get.
There's more but this is a good start