I would probably hate it the most if they took shiny pokemon out of the game. I've never had the time to try chaining shinys like most players, so the number of shiny pokemon i have is relatively small. but every time i encountered a shiny that i was able to catch, i felt like a kid at christmas time. it was like a little reward for all the long hours i've been playing.
so shiny pokemon i would miss the most.
personally, i could care less if they removied nicknaming from the games, because in the 5th generation, they finally fixed the names the way i want them. i always hated how the names used to be in all capital letters, as if you were screaming the name at the top of your lungs, so when i "nicknamed" pokemon, all i did was fix the name so it was proper.