To be fair, every generation has it's strengths and weaknesses:
Gen 1, of course, was the first. Without that, none of it exists. Still probably the best bunch as far as character design goes, although as mentioned earlier the actual game mechanics and balance were heavily lacking, especially compared to later generations.
Gen 2, added more Pokemon, was the first to introduce another region (and the ONLY generation to allow for play in two major regions, exempting the remakes), introduced genders as something other than a way to have two different kinds of Nidoran, introduced being able to be a female trainer in Crystal, day-night cycles (although they've changed on-and-off since then), and lots of other little changes.
Gen 3 introduced, as Manlyspirit said, basically the game mechanics as we know today (EVs, breeding, abilities, natures, etc.), as well as the double battles. It also introduced story differences between the two versions, with the third version (Emerald) being sort of a mix, something that also happened in Gen 4. Sadly, this also was roughly the time we started to get "legendary fatigue", and where the legendaries started to become the main thrust of the stories (although this had sort of started in Gen 2, it really kicked off in this one).
Gen 4's main series introduced the semi-3D overworld graphics (yet still very simple by most any other standard but Pokemon), the Wi-Fi stuff, brought Legendary fatigue to dangerous levels and... uhh..... oh. Right. The physical/special being determined by the move, not the type.
Gen 5 has introduced triple and rotation battles, TMs being endless use, put the Pokemarts into the Pokecenter, let you use repels consecutively without having to pause the game (well, in BW2), did a lot of other little interface changes and had probably the best story in Pokemon's history (which is, admittedly, not saying much). Oh, and it put an emphasis on new Pokemon, which was nice, since it made it at least look rather new. Oh, and it doesn't quite suffer as much from Legendary fatigue as IV.