I get what you're saying, but most of the items that are on the Shadow Pokemon are nice to have. Maybe add in some more variety to items with the Shadow Pokemon that you wouldn't be able to get otherwise and it'll not become so much of that chore?
EDIT: Also to note, if we were to update the game and add more Shadow Pokemon, would we still be able to fight Mirror B at the very end of the game considering we'd need all the Shadow Pokemon catch? That's what I was thinking since the Pokemon would still be available but not catchable in that sense since the trainers would already be beat, such as the Ciphor Peons.