Depends on if we are talking the games themselves or actual pokemon.
In terms of games, it goes the follow, Gen 2, Gen 4, Gen 5, Gen 1 = Gen 6 and then Gen 3.
Despite the insane amount of quality of the recent remakes which I attribute to Gen 6 features living up to their promise (same reason I have Gen 4 over Gen 5, Soul Silver what up), I still think Gen 3 is the weakest.