I'm pretty biased. Gen 5 is my favourite generation, and I think it does have the best plot with Team Plasma trying to liberate Pokemon from humans, and their reasons behind it; N's unique use of Pokemon - not keeping the same team - as he tries to stand up for his own beliefs; the lore behind Reshiram and Zekrom. Team Plasma and N were really interesting, and seeing how they changed in the sequel was great as they weren't just two-dimensional characters. The same goes for the rivals. Cheren and Bianca are kids starting out like you in the first games, and by the second Bianca is Juniper's assistant and Cheren becomes a gym leader as you take on the role of a completely new character. Then Hugh has his own back story and motives. They're not just flat rivals with a little personality sprinkled on top. Hugh actually helps drive the plot forward.
N is probably the most interesting character the Pokemon series has introduced, and I find it hard to fault Black/White/2 at all.