I think it would be best to be able to "mark" a pokemon as a favourite ( by right clicking and pressing "add to favourites" ), it could also add a star next to the pokemon ( i know the shiny star is there that's why you would put it in a different corner and with a different colour.... jeeeeeez ). Marking a pokemon as a favourite would prevent you from being able to release them, you would have to un-favourite it if you ever wanted to release it.
This would also make it easier to find the pokemon you are looking for ( say you have too many pokemon and not enough boxes and you spend 10 mins trying to find the correct pokemon ). Also, you could have a little button at the top of your boxes which when pressed would only show your favourites ( whether it's by highlighting ( them like how the pc filter works), or it just shows them in a box style fashion separate to all of your other trash )