Right now the mod lacks almost every mechanic in Pokemon that remedies these issues: The Battle Tower, and a consistent Pickup ability. While I'm sure this will be remedied quite a bit with the new raid system coming into play, there happens to be another immersive and easy to add feature, that's already in the game, The Kubfu Towers.
The Tower of Darkness and Tower of Waters both already exist in the game, but only as a weak imitation of their games counter parts. While the games have high level trainers leading to the top, the towers in Pixelmon are found completely empty, which gives us the perfect opportunity to make leveling much more convenient and fun. By adding optional trainers with mid-level teams (50-60), you can provide a more immersive leveling function that also serves to imitate a part of the main game. Another mechanic this can provide is an Attack & Defense EV training system as a counter to how Special Attack & Special Defense are farmed in Ghost Towers.
Thank you for your time ^^