Gen 1: The classic theft and power, but wan't heavily integrated into the story. And Giovanni as the crime boss was really great.
Gen 2: I started with 1, but I played 2 the most. I really liked the storyline in this one. Team Rocket returns to make another grab at power. Their take over of the Radio Tower was well planned out, and come on, how about that bait and switch?
Gen 3: It was more integrated, but honestly, the land vs. water debate didn't ring quite as true to me. Plus, the others had a really cool boss, I didn't like the Magma/Aqua bosses as well.
Gen 4: Probably the most deeply integrated into the game, imo, and in the best way. I liked the alternate energy propaganda as a way to gain power and control, and I thought it was well executed. Cyrus was developed extremely well, and he really fit the bill of leader, with lots of easter eggs about the storyline along the way. Space and time was good, could have been better I suppose.
Gen 5: Almost as deeply integrated as 4, but seemed disjointed at times. Have to say, loved the angle of grabbing power through the guise of "welfare" and "equality", especially using N, the golden tongued chosen one. A bit more applicable to current events than most realize I think.
So, the original question. It definitely comes down to 2, 4, and 5. I think if 5's story was integrated as well as 4, I would pick that. But I really liked 4's well placed points. Same with 2, I liked the storyline better, but there were moments in 4 that were just fantastic. Going to the library to talk, and then a bomb goes off, and rushing to Lake Valor. Infiltrating Galactic HQ from underground. I know 4 catches a lot of flak, and personally I don't know why. I loved it, and its what got me back into pokemon after not even buying a gen 3 game.
So, after that book, I'm going to give the nod to 4.