I find the first two Gens to be the best, and I find the latest two to be the weakest. BUT I ENJOY BOTH nonetheless.
in the list below, I don't count the remakes, I only talk about the main games.
Gen IV is the weakest one in my opinion. I just never got into DPPt, and I think they have bad pokemon designs, and is where they really began to over-complicate the designs, which I don't like. I prefer the more simple designs.
Gen V is my second weakest one imo because I don't like N that much, and I cannot stand Bianca one bit. I also didn't care for how the rival battles were handled. It seemed that after each and every gym leader battle, once you left, it would be another rival fight. I preferred the more random ones in the previous Gens. I also didn't care for the pokemon designs. Luckily, the plot in BW were cool, so it isn't my weakest gen.
I also preferred the older gens because of the Evil Team, Team Rocket, seemed to have the most realistic goal out of any of the others. They wanted to get rich and steal, not do ridiculously over-the-top things like expand the land, expand the sea, control time and space, etc. Having said that, I thought Gen III (Especially Emerald version did the evil teams' right despite having the ridiculously over-the-top goals)
It is all personal preference in the end. If you started late, like if Gen IV was your first gen, you are more than likely going to love the more complicated designs a lot more than the more simple designs of the pokemon of the early days. If you started early, like me, with for example, Gen I or II, you are more likely going to love the simple designs a lot more than the complicated ones of today.