I kind of addressed this over here.
The current item/pokemon storage system mirrors that which was in the handheld games. Unfortunately that is inefficient given the vast differences between the 2 play styles. We are catching monumentally more amounts of pokemon than we ever were/did in the handhelds. There has to be a better way to manage those catches, so that bag/space management doesn't become the entirety of the game.
Nobody wants to spend hours upon hours discovering IVs and transferring fodder. We need a better system/mechanism.