The appraisal system is wack... it just is.
I am catching far more pokemon in Pokemon GO than I have over the last 7 generations of the classic games. I typically catch more in a week, than I caught in any single game.
As Pokemon GO is unique to the franchise, it's creators must develop unique management tools so that we spend more time playing the game, than filtering through our collections determining what to keep and what not to keep.
My personal opinion. Its time for hidden IV to go away. I need to be able to quickly identify which of my 'mons are the best. Additionally, I need to be able to select them a lot easier. I need to be able to flip the current filters. Example A-Z and also Z-A.
Other ideas would be things like auto-transfers for a given set of parameters. Like not keeping anything below 50% appraisal.
With gen 3 already in the game files, and could release literally any day. I find it a little concerning adding another 135 pokemon to the mix. Adding more bag space isn't really a long term viable solution if I am being bogged down by constantly trying to keep my bag below 1000, I'm going to have even more issues if they increase it to 1500. Gen 3 of the classic games had a max pokemon storage of 1500, but as mentioned earlier, most of us weren't catching 'mons at the rate we are in Pokemon Go. Management needs to be addressed.