I think in terms of balance, variety, and new features added, Gen III takes the cake. A lot of people were upset when it came out because it took away a lot of pokemon from the previous generations (locking them away until the post-game or until colosseum/fr/lg came out) but I think the new Pokemon added more than made up for it. Pokemon Emerald is extremely replayable and the Battle Frontier offers a post-game that goes on indefinitely while providing plenty of challenge. Also Gen III added abilities, which is probably the most important gameplay addition/change next to the Physical/Special Split of Gen IV. Also, Gen III didn't run at a snail's pace like the later games (I'm looking at you Diamond and Pearl).