You should really check out Pokémon XY. the game is really good even though there aren't many things to do after the main story ends since there are only 3 other legendary pokémon you can Catch.
Since Silver a lot of stuff happend, going gradually:
-Now Pokémon Have abilities that can help them in battle (some of them are useless and some are even bad like Slow Start);
Now Pokémon can affect the Weather, the Weather can be: Sun, Rain, Sand Storm, Hail, Heavy Sun and Heavy Rain (this last 2 are missing in Pokémon X/Y);
-There are double battles where you use 2 Pokémon vs other 2 Pokémon;
-Now there are Pokémon natures, IVs and EVs, all of which affect the pokémon stats, but they only matter if you want to play at a competitive level;
-Now Pokémon Types aren't always special or phisical, every Type has both phisical and special attacks;
-There are 3 vs 3 Pokémon Battles where you can either use simply 3 pokémon and chose a move for each one of them or in another format where you have 3 pokémon but one of them is in the front of the other 2 and only the one in the front can attack, you can either chose to attack or to rotate the battlefield and attack with one of the other 2 pokémon depending on what you think the opponent will do;
-There is a new Pokémon Type, the Fairy type, some pokémon have completely changed into Fairy (Clefable), some other have mantained their original typing (Jigglypuff Normal/Fairy).
-Now there are MegaEvolutions. A special form that ONLY ONE Pokémon of your party can get for each battle, this evolution increases stats and sometimes changes types and abilities, after the battle ends the Pokémon return to their original form