So this may have been mentioned somewhere else, and my apologies for not seeing it. I typed in the keywords 'PC Box' to find some thread on this already but didn't have anything pop up.
Anyway back with the actual suggestions.
1) having a Box or two dedicated to pokemon a person actually uses/wants to keep:
This will allow a player to not have to search through every single box to find the main pokemon they use. Drag/dropping them to place them in last place has been the only real way I could relatively easily find my pokemon i use to actually fight with, and that can be tiresome as I start to want to catch all the pokemon which will get dropped in the boxes.
2) Have the ability to Organize the boxes themselves via various filters:
For example you could organize them via level so you could find your main pokemon that way, assuming they are your highest level which is likely since they will be the ones you use the most anyway. Or perhaps filtering based on friendship might work since it's also just as likely the main pokemon of a player will have the highest friendship.
3) Have a method to 'label' a pokemon in the boxes:
perhaps while inside a box, a player could right-click on them to mark them as favorites or as their 'battle' pokemon. Or something to that effect.
These are just my suggestions for a quality of life change to the PC Box system. I don't know anything about programming and stuff so idk how hard it'd be to implement any of these, but I think it'd be kinda cool.