It's a simple idea though. It could be either an add-on or an option in the game where you can select an encounterable pokemon (e.g. i'm farming at Route 1 and I want to catch a shiny Rattata, so I choose it via this add-on/option) and a counter with an icon or text of the selected Pokemon appears and starts counting how many times you have encoutered that specific 'mon. As a hunter I always like to keep track of my encounters but when I'm looking for something special or extremely rare, it's easy to lose it after a while.
It's not a high priority one, but I'd love seeing something similar in the game in the future. :)