Also, it's really hard to train your Pokemon in the early game, because it's rare for wild Pokemon to spawn at level 5 or below, and trainers are extremely rare. It's also quite difficult to make money.
To avoid the XY problem, I'll come out and say I guess the feature I'm really requesting is a solution to these gameplay complaints; any solution will do, I'm sure. So the following three items aren't exactly the features I'm requesting per se; they're just my own ideas on how the gameplay adjustments I'm asking for could be implemented.
1) Wild Pokemon could pose a threat to the player, like in Legends: Arceus. Say, for instance, if the player's Pokemon have all fainted, and the difficulty setting isn't peaceful, then whenever wild Pokemon try to become aggressive, instead of their aggression being cancelled because the player can't battle, it instead gets turned into hostile mob AI. Contact damage, as with zombies, would be plenty good enough as far as implementation is concerned, but ranged attacks with animations would be very cool, even if it's just colored particle streams, and even if it's just the same attack for every Pokemon except the Pokemon's primary type determines the color of the particle stream, and maybe the level and special attack stat determine how many hearts of damage are dealt. Anyway, the point is, making wild Pokemon dangerous would kill two birds with one stone: it would alleviate some of the morbidity and guilt around the wild Pokemon's implied death upon defeat, and it would make the vanilla health system and survival gameplay relevant again. Additionally, it would lend purpose to the config option that allows the player to personally attack Pokemon (which existed, if memory serves, though it might not) and restore purpose to crafting weapons and armor.
2) Sell prices could be assigned for certain vanilla items. Particularly vanilla items that require a great deal of vanilla gameplay to produce in bulk: foodstuffs, rare minerals, enchanted books, effect potions, etc. This would reincentivize vanilla gameplay by creating a pipeline from vanilla gameplay to Pixelmon-related benefits; a player could, for instance, spelunk caves for coal and iron, craft iron tools, spelunk farther and/or strip-mine, and obtain diamonds and/or emeralds, all to sell them to Pokemart shopkeepers for hefty amounts of money with which to buy TMs and high-tier battle items, or just to stock up on mass amounts of lower-tier fundamentals like potions and Pokeballs. As this is already possible by editing the external JSON, I already have this functionality in my single-player game and am enjoying it.
3) If the default spawn rate for trainers were drastically increased, it wouldn't be so difficult to make money. It would also be easier to train your Pokemon in early game, as I've found trainers seem to be more willing to spawn at low levels. Since this, too, is already possible by editing the external JSON, I already have this functionality in my single-player game and am enjoying it. I increased the spawner weight of all NPCs by a factor of 20. They still spawn less than wild Pokemon do. That's how rare they were to begin with. Alternatively or in addition, it would be nice if it were more possible to find wild Pokemon at or below level 5.