Every pokemon vary in shading color and size and if it has patters, they are random too. This is very easy to do now with 3d models. But must be something very slighty, barely perceptible, just for making every pokemon more unique.
If the attack is more powerful because of weather (like surf in rain), it's animations is slighty more brighter/darker/longer/bigger/fierce.
Critical hits are followed by the pokemon cry.
IVs does not have a relation anymore with atributes. Now they are personality values. They still go from 0 to 31, but they work like: 0 is a lazy pokemon and 31 is an hyperative one. The personality values affect slighty his battle performace, a lazy pokemon sleep for longer but rarely hits itself when confused, for example.
The NPCs and trainers in routes and cities varies with the day of the week and the level of the pokemons of the trainers scales with the number of badges you have.
Some trainers have random pokemons that are set when you start a newgame. The items dropped that are not unique (like TMs) are also all random, but always balanced. You'll not find a max potion in the start, but can find a potion, a oran berry or a pokeball.
Along with shiny pokemon, there are albino pokemon. They are as rare as a shiny, but they have high chances of breeding another albino pokemon. Also, some pokemon does not have an albino form, like ditto and legendaries.
Some attacks have different visual effects when used by pokemons of different egg groups. Double slap for example looks like hands when used by most pokemon, but when used by dragon egg group, it looks like a tail.
STAB ice attacks have a natural 20% of chance of freezing. If the target pokemon is water type the chance goes to 30% and if it is under the effects of aqua ring, 50%
Physical fire attacks burn ou ingrain and leech seeds.
Hurricane, Gust, Twister and other wind-based attacks blow away entry hazards. Explosion and self destruct also does, and the power doubles if there is any.
