It's not a big change but I preferred how some of the monsters' designs looked in their first generation sprites.
Now, a big one? Effort values; I hate how they're used in competitive to minmax monsters when the original intention appears to have been simply to make them all unique individuals, to give monsters more personality and depth, but they've just become a means of specialisation to absurd degrees. I like watching competitive anyway, but would certainly not enjoy partaking. I've EV-trained something myself and in the end it just feels hollow to use.