It would be nice to have a feature to cap the levels a wild pokemon can have (e.g. a range 5-25) and maybe also a feature that will increase the level cap the farther away you are from the world spawn (level per block where block is the distance in blocks from the world spawn).
An alternative is a feature that will modify the catch rate based on your highest level pokemon in the party. There could also be a hard cap based on the highest level pokemon in the party that makes it impossible to use pokeballs if the enemy is 20+ levels higher.
Another alternative is the badge system used in the original games, giving a pokemon random chances of refusing to make a move based on the badges you have and the level of the pokemon (which badges that should be used could be a configurable list of items IDs).
All of these should be able to be modified in the config ofcourse.