My personal favourite generations were the first and second ones. These two were really special, and they actually followed a simple, yet interesting plot.
The third generation on the other hand felt so empty to me as it was quite different from the previous two games. Generation 4 was ok, but not as great as the first 2 gens (though I must admit that HG/SS were really good). Generation 5 is probably my favourite after generation 2 as it is definitely quite unique with a lot more interesting Pokemon.